It's always tricky having GI Joe and Transformers coexist in the same universe because the latter element escalates things immediately. It's hard to isolate and ignore it for the sake of telling GI Joe stories. They're the elephant in the room that always has to be acknowledged because why would a special military strike force not be deployed to deal with this sort of thing?
Unless you keep it to early stages of Infiltration protocol, and culminate with the GI Joes or Cobra or both stumbling upon the facsimiles used by the Decepticons. But from there the state of play has to change. Transformers becomes the Poochie of the world GI Joe inhabits.
Which isn't bad per se because there's plenty of stories to be told with that interaction, but it's a pervasive undercurrent for GI Joe stories that will have to be accounted for. Just shared universe things.
Marvel has been doing it with the Avengers for ages now. Why wasn't the Hulk or Thor or Iron Man called in? Oh, they're in space. In the end, it's still a big planet and humans are still gonna "human" leaving plenty for the Joe team to do.
If nothing else, the fact that these aliens are able to convert at will means most "action" can appear anywhere and disappear just as quickly leaving even the Joes unable to respond in time.