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PKHeX doesn't cause lags, that's just how the game is.

Keep in mind is a rare scenario. The only illegal moves in this scenario will be moves that a Pokemon can only learn after evolving but can't learnt it on future generations. Most Pokemon does not have any move with those two caracteristic, exclusive for an evolved form and exclusive from previous generations, both at the same time. And it should be a Pokemon that can't evolve on any level like those who use evolution stones. For example, Jolteon in gen 5 has a move hat Eevee can't learn nor Jolteon can't learn during gen 5 but given Eevee can evolve into Jolteon at any level the move will be legal at any met level.