Face value based on on-panel stuff and the writer's commentary. The connection between Bay comics and the BB movies lacks that. That is the basic difference between the two. The CJ comic thing can't be equated with what you are saying. Simple as that really.That's not what it says exactly, though.
These are out-of-context anecdotes written by the poster on the wiki, not quotes from the writer.
Nowhere does it explicitly say that they used the designation of the IDW comics to distance from Bumblebee. That's inferred from a second-hand account. That interpretation is something you might think based on what someone said about what someone else said.
What we see in the comic, more importantly, is:
1. All realities are the same designation as the continuities that they branch from.
2. The Bayverse should, as a result, be a branched timeline from the original continuity.
3. It branches, very specifically, from the events of the Bumblebee movie. This isn't really arguable, it's what the comic literally shows us.
4. The designations are based on medium rather than universe, so really, the "Gamma" part doesn't make it a separate universe to Bumblebee.
I personally just find the reading that it is the same universe as Bumblebee and they're branching off from it more consistent with the story. Even if not, it still implies that the exact same events from Bumblebee were happening no matter what reading you ascribe to it.
1.) Because here, the writer didn't think of them as branched timelines but actually changing the timeline according to the TFWiki link from someone that talked to the creators (I said to ignore the timeline changing originally since erasing the entire shows of G1 and Aligned wouldn't really stick, but this was indeed his intention).
4.) Often they use it interchangeably (look up the AVP stuff where they sometimes call streams realities, universes etc.) And in here, the writer did use it to mean realities. Again, the creator already explained his intention here.
I won't address your other points because I basically already addressed them before and I don't wanna be here arguing all day.