I thought the New Avengers/TF crossover was a separate continuity. In the Marvel Universe the New Avengers occur on Earth-616 which is the "mainstream" Marvel universe.

Now I doubt that Marvel would allow the New Avengers, Dr. Doom etc. to enter IDW continuity... so I think that Avengers/TFs must be either a contained continuity or perhaps Transformers entered Earth-616. The former seems more likely to be the case... considering that Marvel didn't allow Transformers to exist on Earth-616 during G1 and G2 when they publishing Transformers, I am skeptical that they would allow it now that TFs is no longer in their court.