They could technically explain away they were never in the MCU if they wanted to, as parallel universes can be similar but a little bit different in other ways. The show does keep referencing 616, which has ties to comics and not the movies, and it is the only part of the MCU to do this (as far as I know). That reference is usually an easter egg, but they could do more stuff with it if they wanted.
I still really want the second arc to be a universe hopping arc. The whole first arc could still be a slow realization they moved universes, not just in time, and the second arc expands on that. I am not sure how Fitz would also have moved with them, but that can be explained away later. The flashbacks from the last episode also make sense if they were a parallel universe, as does Robin's powers.
"Ultimate Agents of Shield" has a nice ring to it.