That seemed to be a all-the-way-from-the-top issue, as the "Transformers" title was minimized in the Beast Era on both the shows and the figure packaging.
It's somewhat comparable to how Enterprise was just Enterprise in its first two seasons, prompting fans to wonder if someone in production was purposefully avoiding drawing connections, and if so why that was....
The funny thing is that Bob and Larry weren't shy about making connections to What Had Gone Before, once they found out about it. And while they didn't quite have the resources, Mainframe seemed to relish the challenge of bringing the MTMTE cast and "sets" back briefly in their Agenda flashbacks. So if the creative end wasn't embarrassed by G1 (or even G2) connections, who in corporate was, was the question at the back of some minds?
Probably because Beast Wars was put out initially by Kenner, rather then Hasbro proper and G2 had just came and went. This was probably something akin to Nintendo not wanting the DS linked to the Gameboy; new line of transformers, that weren't mechanical or vehicles? Lets hype it as its own brand BEAST WARS transformers That way if it failed, it was just a distant cousin to the brand like Animorph toys were. A sub brand put out by a subdivision, no one wanted touch the main line that had just had it second breath.
As for creative side, they initially wanted to also distance themselves from the original series, acknowledging it while wanting to do their own thing; until the fans started talking and they quickly changed their plans to be "yeah sure, why not?" in the midst of making season 1. It's pretty much because of fan input that we got a lot of the Easter eggs and nods, and eventually The Agenda. The series would have probably been VERY different if not for early internet fandom.