I believe the following will FINALLY put this button issue to bed.
TLDR: Sega kept changing pinouts on their System 16 hardware. So some games had buttons swapped, other didn't.
I spoke with Adrian (PCBJunkie) who makes adapters for System 16 and asked his opinion on why there were so many discrepancies with the buttons on Sega games.
Here's what he wrote:
"Sega can't even keep their own button order consistent. There is no way to create a single adapter that will have the correct button layout for all Sega games, unless button remapping is used. I'll just give you examples with these 3 button games that I'm pretty familiar with (below). Two button games often use button 2 and 3. Alien syndrome (1 button game) uses button 2 only... lol
Manual: special, shoot, jump (connector button position 1, 2, 3)
Sega CP: shoot ,special, jump.
Button Order: 2, 1, 3
manual: magic, attack, jump
Segla CP: magic, jump, attack
Button Order: 1, 3, 2
manual: Jump, punch, kick
CP: punch, jump, kick
Order: 2. 1. 3
So there you have it. Best bet is to get an adapter with the jumpers for flexibility.