I also feel the contradictions can just be explained by different religious sects. Like, amongst people who worship Primus, some of them are believers in the Guiding Hand, while others believe in the 13, and still others just think Primus just created the cybertronians directly, no intermediaries or avatars.
Some believe that Primus created Cybertron, while others believe he became Cybertron.
Perhaps in ancient times, the 13 were each worshiped individually; like, say, Solus' followers didn't believe her to be a creation of Primus (or had even heard of Primus), they believed her to be the creator: period. The diety who, in their creation myth, ripped a massive hunk of molten metal out of a star with her bare hands and forged it into Cybertron.
Meanwhile there are those who believe cybertronians evolved from naturally occurring pullys, levers and gears, while still others believe the planet was created by mortal hands, though for what purpose eludes them. Perhaps intended as a slave race, or perhaps they arose from an abandoned factory world left to it's own devices for millions of years.
The important thing is, nobody who was around for Cybertron's origin is still around now, and they didn't leave any concrete details behind. All they have are contracting fables and faiths from all over cybertron. It's works very well as flavor, as well as paralleling our own search for answers.