I think the DW G1 comic/toy overlap was largely coincidental, in that G1 was experiencing a huge revival at the time and both avenues were being used to cash in on it. They weren't actively promoting one another (beyond ads and blurbs). Sure, there'll be some cast crossover, but it's not like either was NOT going to use Optimus Prime or Jazz or Bumblebee. I think the toy half of things was just not at the level yet that it could even do that -- first of all, it was a reissue side line to pad things out, not something they were actively developing and investing in anew. They were finding out what molds were even available, verifying what safety-rule-mandated changes were needed, and so on. Plus the brand team's priority was the main line (I miss the days when some flavor of G1 was not the main line) which DID have a comic explicitly promoting it.
At most, Hasbro and especially Takara (with the gorgeous book-box reissues I sorely want to see revisited) leaned into using the artwork for a lot of stuff, but that was it. It wasn't like Shockwave being the big bad of War and Peace was accompanied by a Shockwave reissue. (Even the Alternator was a year away from the tail end of the ongoing where he showed up again, and even that would've been a streeetch.)
To use a metaphor, they weren't playing together, more like parallel play.
The comic buying public is used to stand-alones and one-offs and mini series. I don't think it would have been an issue.
I don't disagree, but I think I was considering it more in terms of IDW as a publisher with perhaps smaller margins than the traditional big two -- and at the time they already had a number of things running alongside the "main" books, which were already two books. Churning out another book per month might have not been seen as a good use of money (debatable), considering they also had Revolution and TAAO and other events and series going. And the movie books had themselves gotten wrapped up before even AOE, meaning one less non-IDWG1 continuity being published. (This is why I thought of shorter "backup" stories in each issue instead, but that would have complicated page allotments for the main book and for ads and whatnot.)
Plus I guess an alternate-continuity thing was not exactly something Barber would have entertained at a time when they were deliberately welding together a big sprawling shared universe. (The alternate-continuity part of my suggestion was specifically so that their main G1 stories could proceed unaffected by new stories and plot devices and maybe different characterization for guys like Chromedome and Krok.)
(I mean, they did years before this put out a bunch of miniseries set in Aligned, so it's not like they were always averse to this.)