It wasn't Marvel who did these. All the "remastering" was done by IDW, in the 2010s.
Well that's my point, it's an industry problem, not a Transformers or Marvel problem. Comic companies mess with reprints all the time, and it's annoying.
Yes, and I'll add that my favorite approach to TF theo-mythology was how Roberts handled it for most of his run, letting the facts about Primus and the Guiding Hand sit in limbo and giving space for characters - and the audience - to interpret things in various ways. One of my disappointments at the end was how he made things anticlimactically literal. (Part of the anticlimax was the super-rushed pace, but still.) [Edit:] And just to show that I'm not only against TF gods being portrayed as literally real, I also wasn't a fan of the way Barber fully demythologized the Thirteen. Ambiguity can be a good thing!
I'm so mixed on how IDW handled the mythology. There's a lot I like! I'm a Euhemerist at heart- the idea that all, or at least most, mythology has some kernel of truth to it, and IDW leaned into that. The idea that the Guiding Hand, the Knights of Cybertron, and the Thirteen were all real, and had their deeds mythologized over time to the point that they became deities, is so interesting to me. As I said, it's an approach I think holds a lot of weight when studying real world myths and religions, so to see Transformers' mythology treated that seriously was, well, a treat.
Further, it seemed like they were on the cusp of pulling off what could have been the single best merger of the Sunbow and Furman Marvel backstories. The Lost Light, over the course of their adventures, find the actual mould Cybertron was "made" in, and between that and the revelation that the pantheons were real, and that Primus himself had a serial number... seemed to be leading to the idea that the Quints made Cybertron and the Cybertronians, and that perhaps the rebellion that freed them from the Quints was the start of the stories that would be mythologized into the broader Cyberyronian mythological cycle. Basically taking that Euhemerist approach to its logical conclusion in the franchise- the Sunbow origin was the kernel of truth, and the Marvel origin was the myth that grew up around it.
Sadly a lot of those ideas were never fully explored so we're left with conjecture, but it seemed to me that's where they were heading.
But as much as I appreciate all of that... Roberts still made his self-insert OC Robot God, and I feel that has to be talked about more

it would have been rightfully torn to shreds if it was posted on Watpad.
Regarding ambiguity... I like it a lot, honestly. Tolkien flat out refused to explain Tom Bombadil and his explanation that sometimes the storyteller needs to keep some things a mystery is a lesson we need to take to heart in our modern age of fan wikis, YT lore channels, and direct access to creators like never before.
Sometimes it's ok if not everything has a clear answer.
I don't begrudge Furman for introducing gods - in fact, one of those unexplored areas that actually does intrigue me is how the Keeper said Primus and Unicron had been part of a larger pantheon in the pre-Big-Bang universe. What was all that about? But, as you say, the Primus/Unicron mythos is too easy a go-to for filling in the gaps in every continuity. The multiversal-singularity thing didn't help at all; thankfully that's been nixed.
One of my favourite Doctor Who episodes involves the Doctor meeting the literal devil who tells him he's so old he's from before the Big Bang and the Doctor can't believe this, he can't accept it, but the TARDIS can't translate the runes in the devil's prison and the devil very clearly upsets the Doctor by telling him that there are aspects to existence even his knowledge as a Time Lord can't fathom. It's the perfect mix of myth, teasing out info, but not saying too much. It also touches on this, the idea of gods and devils existing in a universe prior to our own. It's such a cool idea. And given that Hasbro used Furman's stuff as the basis for so much of their myth making... they ignored the most intriguing stuff!
That, however, leads me to agree with you. I don't dislike theistic myth and fiction, hell I enjoy it if it's done well (see the example I just gave). But Furman's mythology, at least the bits Hasbro seized on and emphasized and built on, is too easy. Not just as a plot device, but as a mythology.
It's baby's first Zoroastrianism, a massive dumbing down of the concepts of Ahura Mazda and Angra Mainyu, with a sprinkling of Judeo-Christian Messianic theology atop of it.
And while I find Roberts' writing on religion to be a bit too simple from an atheistic perspective, I find Furman's too simple from a theistic perspective. I'm a historian and a theist myself, and religion is a messy business, be it historically or as a matter of belief. It's complex and untidy and even when you have ideas such as ultimate good vs ultimate evil as cosmic forces, these are often shrouded in metaphor, morality tales steeped in the ethos of the time they were written, and layered understandings of theistic belief that can shift depending on who's interpreting what. Furman's mythology is just... too neat and tidy. Which is one area where I appreciated IDW's work, making it seem like it was layered and ever evolving as Cybertronian society progressed.
Sunbow, by contrast, gives us something entirely unique. Sure it reeks of its time- authors in the 80s playing with ideas and tropes from the 70s- but what it creates is enticing, dark, and mysterious. It manages to strip away the godhead and fully explains the creation of Cybertron as a mundane act of consumer economics, and yet has this underlying mystery and mythological elements that add to the unknown. We know there's no Robot God who just made everything in his image, so how is the Matrix explained? It's just as supernatural as it's always been, but that mystery and the potential for worldbuilding is greater BECAUSE the easy answer of Primus is off the table. How does a race of squid aliens, their consumer robots that gained sentience, the monkey alien scientist, and the Death Star he created all tie into this mystical artifact? It's such a juicy proposition. I have my own fan theories but it's not really called for here... but that's the fun, right?
One last thing - I also really like your description of the flavor of sci-fi Sunbow was working with: "Kinda trippy, kinda subversive and dark, but not in a gritty way." The limitations involved in being a kids' property in the '80s helped, I think. I mentioned in my first post that I could go on about all the positive qualities of FFoD, and one of those is how it stayed within those boundaries but played at their edge. Like, you know that in a less constrained version of the same story, Galvatron would've been more explicitly murderous (poor Sweeps), but I don't need horrible things shown to me literally to get the narrative idea. And there's still room for conceptually dark stuff. The final line - "We Transformers have looked into the face of our creators and seen the face of an enemy" - is hard af. I wouldn't want every take on TF origins to be that dark, but retconning a benevolent deity into that one takes something away from it, imho.
Sunbow, particularly its Transformers stuff, had such a vibe that's almost entirely absent from the modern franchise. Even the stuff that's trying hard to homage it or lean on it can't get it right.
The haunting melodies on Cybertron, the goofy aliens, the whacked out designs... it all feels truly alien and disconcerting, like this world's universe is vast and almost unknowable and what bits we see of it beyond the immediate action are either totally odd or off putting or terrifying.
Or sometimes a giant alien child plays with Soundwave like a toy, or Starscream tries to take over Camelot

Sunbow could be all over the place, but it had something special when it locked in and focused on the cosmic stuff and the mysterious of its own backstory.
To be fair to that contingent, my impression based on zero hard data whatsoever is that Roberts' run did more to bring in new teen and adult fans than probably anything besides the Bay movies. The nostalgia market will always be strongest with fans' "first love". The same principle probably applies to Marvel vs. Sunbow - I expect most people who got into TF in that era did so through the cartoon. (I get the sense that that was flipped in the U.K., but that peculiar little isle would need to be a bigger slice of the market to move HasTak's needle.)
Oh I'm not being critical. Everyone has that special entry point, and everyone has that one thing that's very special to them and they wanna see it done right. IDW fans feeling that way about it totally makes sense.
I just think that the nature of IDW vs the nature of Marvel G1 leads to IDW's audience being harder to entice, so you need to lean into it with more dedicated product. Whereas Marvel G1 fans by and large don't need dedicated Marvel G1 to buy in.