If I use an Atari 800 core there is only 1 game I would want to play on it. That is M.U.L.E. with all 4 joystick ports at a M.U.L.E. party. The C64 version has much better music but 2 of the players must use the keyboard during the auctions. Letting everyone have their own joystick on the Atari 800 is much kewler.
We would plug in all 4 joysticks into the Replay... woops... there are only 2 joystick ports.... Ok so obviously the Atari 800 core, being highly professional and containing all needed features, would look to the daughterboard for the other 2 joystick ports.
My Elite 68060 daughterboard should supply joystick ports 3 and 4 because a bunch of Amiga games use them... but it does not... so the Atari Core just starts sending out a bunch of signals that make no sense to my 68060 daughterboard and everything would then go berzerk.

This is what I am trying to avoid.