I did these tests by taking BlastEm's source code and modifying the mouse output to feed wrong values for those two bytes. This means I couldn't test any Mega CD games though, so it's possible something got missed :/ (anybody willing to test those is welcome)
Games tested:
- Body Count
- Fun'n'Games
- Janou Touryuumon
- Jimmy White's Whirlwind Snooker
- Lemmings 2
- Lord Monarch
- Marble Madness (Tengen)
- Nobunaga no Yabou
- Nobunaga's Ambition
- Richard Scarry's Busytown
- Shangai II - Dragon's Eye
- Two Tribes - Populous II
- Wacky Worlds
As for everything else… they all Just Work™. Yeah, all of them ignore whatever is in those two 1111 nibbles, they only care about the 1011 one. On the other hand, SGDK seems to want all three nibbles to be exactly 1011 1111 1111 (whoops)… Looks like the packet is just ignored if they don't match at least (instead of completely dropping the mouse), though it also will look as if no buttons are pressed. I hope there isn't much breakage out there if somebody decides to add mouse wheel or something in their own version of the mouse (・-・;)
Most games need (and/or can take) the mouse in the first port. Fun'n'Games is the exception, requiring it in the second port (and a controller in the first port, which you need to get past the title screen).
tl;dr
- The two 1111 1111 nibbles in the mouse packet are meant to be ignored and only the 1011 should be used for identification. Do not rely on the 1111 1111 nibbles to detect a mouse.
- Changing the values of those two nibbles doesn't look like it'd break anything significant, which may come in handy if somebody builds an adapter or builds new mouses and wants to add support for mouse wheel or whatever else (a way to toggle extensions off is probably still a good idea).