They will not be part of any assignments or anything else.
Does that mean the start-of-season assignments will not require going to the infected areas that mission control praises you for braving in said assignment?
I was not completely clear, sorry. I meant the auto-generated assignments and assignments that are looking for missions with random warnings.
The season assignment specifically looks for missions with the lithophage warning and as such you would want the seasonal content activated for those, otherwise it could take a long time to complete them as you will rely on rng to create a lithophage mission which is not very likely.
That said, I would expect most players who reach lvl 100 in the performance pass have also done the initial season assignments...