I'm surprised this thread has seen so much discussion. The answer is NO. Altered Beast shouldn't even factor into the equation. Whether a CD system can run a Tennokoe Bank Hucard is a heck of a lot more important than its ability to play Altered Beast.
All one has to do is make sure their CD system can use any necessary system cards.
If someone wants to play the one terrible game that requires the 1.0 System Card (which was only released in Japan), they'll need to make sure their system can run a Japanese Hucard (i.e. play is on a PCE or on a U.S. deck with a converter or region mod).
If you want to play the twelve ACD games, you'll need to make sure your system can handle the Arcade Card Duo or Pro.
Same for GameExpress games.
Necro and Sunteam - what are these several games with incompatibilities you've hinted at? If there are actually any others I'd really like to know.