After all of the talk over the last year about should it be rebooted after the mess of TF5 (and arguably the 2 or 3 before that), this actually doesn't surprise me. I know that Bay doesn't worry about story continuity, as he focusses on making each movie the best stand alone action-explosion movie possible... but the creative team (writers, producers, directors) that now have to create stories around all the contradictions and plot holes of the past, because they would want to focus on their movie having a good story that makes sense to the audience (who shouldn't need to be distracted by special effects every five seconds just to get past a bad scene or story element).

And when Hasbro announced a combined cinematic universe, it was always going to be a pretty good chance that they would include their most successful brand (Transformers) in some way... now they can, if down the track, it is rebooted as a new alien threat in that series of HCU movies (first contact with the earth, who would now have special military teams (GIJoe) and maybe an earlier alien threat (if one of the other HCU movies gets done before the next TFs) to be prepared for a massive alien robot invasion.

As much as I would have like to see where the Bay-verse was going with Unicron, I just didn't see it having much potential as the core of the Earth... because fans would want to see him transform, and that certainly wouldn't happen without destroying the planet. (but I'm sure Bay would have made it possible to repair the earth with some sort of Cybertronian gadget, as if nothing had happened).

I'm sad that it means that the first two movies now also have to be lost in the new Transformers universe (or HCU), but if it means a clean slate to rework a new story foundation (like the original cartoon bible), then it can't be worse than what we got from Bay.
I'd just be worried that if Transformers is part of the HCU, and the HCU fails, it will affect Transformers as well.