Again, mutants being a new phenomenon to the MCU doesn't mean there can never have been any mutants throughout history. It doesn't mean the entire species has to be new. It just means the public never knew about them before. None of the characters you just named would in any way be a problem in that regard.
Sinister, Apocalypse and Selene were always portrayed as being far older than the known existence of the mutant race. Wolverine, too. And Sabretooth. And every other mutant I can think of who is older than Xavier and Magneto. And really, since Xavier originally coined the word 'Mutant', even their generation predates public knowledge of mutants. None of them would have been called 'mutant' in their early lives, only 'freak' or 'demon', etc, and to the extent that they were known to the public they would go down in history as mythological beings or urban legends. Some of them might have had history with SHIELD, just like Ant-man did, but that would also by definition be kept secret.