Actually, if it had happened that way, you'd never have known the difference.
Had Phase II become a reality, there would have been no TMP, because the pilot episode for Phase II became TMP. Everything else would have been changed also. So, if you'd seen phasers being fired from the "neck" of the ship, after only seeing TOS, then it would have been no more weird than seeing torpedoes fired from the "neck" in TMP, because both weapons were fired from the saucer in TOS.
