They are not punishing you.
They are testing things like squads and progression in the second alpha, the reason assignments are turned off is probably because that's not what's being tested, why waste time enabling something which is not being tested.
There might even be another reason. Perhaps the assignment system in this alpha version has bugs that could interfere with the testing of the changed progression system, I think this is very likely. I guess they could not have let in new people for this alpha to avoid people asking for the assignment but I figure you don't want that either.