The Bumblebee Movie Prequel considers Age of Extinction, The Last Knight, AND all the IDW material canon.
According to the Transformers wiki:
#2
The idea that Sector Seven's ranks may potentially have been infiltrated by Soviet spies hearkens back to IDW's Transformers: Sector 7 mini-series, which featured an adventure set ten years before the events of the Bumblebee prequel in which defector Joe Danco stole S7 secrets for the Reds.
#3
Now we're getting into that rich, creamy, IDW movieverse history!
Astrotrain goes unnamed in the issue, but it's hard to imagine the character is meant to be anyone else. This IDW-original character first appeared in the Foundation and Rising Storm mini-series in 2011. His being on Earth in the 1960s doesn't particularly contradict anything from those series, as he just sort of popped up out of nowhere on Earth even then.
Heath Donavan is the son of Sergeant Donavan from IDW's Sector 7 #4.
Donavan's jet is strongly hinted to be Jetfire, who we know from both the Sector 7 mini-series and Tales of the Fallen #3 was active and roaming the Earth at this point in history, having not yet entered the state of stasis he would be found in during the Revenge of the Fallen movie. See "real-life references" below for notes on his alternate mode.
#4
Malignus refers to "Earth's not-inconsiderable cache of Cybertronian treasures," alluding to the many, many Cybertronian artifacts that have turned on the planet over the course of the film series, including the AllSpark, the Matrix of Leadership, the Star Harvester, the Ark and its space bridge pillars, transformium, and the Staff of Merlin.
Bumblebee remembers fighting alongside Diabla in the smelting pools of Altihex. The famous pools were established to be located near Altihex in live-action movie continuity by—of all things—the friggin' Transformers version of the Risk board game.
Astrotrain flees mid-battle, leaving him alive to eventually reappear in IDW's Rising Storm series, set between Revenge of the Fallen and Dark of the Moon. As he goes, he comments that "even Shockwave never treated [him as] badly" as Malignus, referring to his time under Shockwave's command back on Cybertron, as seen in Rising Storm #2.
Bumblebee's pursuit of Blitzwing was evidently intended to lead into the beginning of the Bumblebee movie, which features a fight between the two early on. However—whether as the product of last-minute changes to the film, the comic being given an outdated script to work from, or some kind of active disinformation—the film does not flow out of what we see here; rather than Bumblebee tracking Blitzwing down, it's Blitzwing who hunts Bumblebee down, not after twenty years, but immediately after his arrival on Earth in 1987.