In another thread someone said WHDLoad patches the games to support the CD32 pad, that's why the Sega pads don't work.
I am not saying you are wrong, but from what I know from those pads, it's really weird that it wouldn't work with the Mega-Drive pad.
I have a few DB9 male/female connectors around here, I guess I could easily build an adapter to make the signal going through the DB9 connector to be identical to the Master System one (I think you only have to cut the +5V and the Select cables).
The only Master System pad I have here to test is a 6 button thing made by Tec Toy for a certain Master System model they produced, where A and B is button 1 and C is button 2, start pauses the games (this model has no pause on the console) while X+Y+Z is used to reset it. Master System pads are hard to come by. I wish I still had my Master System joystick that I bought the same day I got my A600 back in 1992
This controller works finely on classic Master System or even on a Mega-Drive running Master System games (even on games that go crazy with the Mega-Drive pad like Wonderboy in Monster Land ) but without the controller pause or X+Y+Z reset working. I have no idea how this X+Y+Z and Start is sent through the DB9 connector and I am really afraid to plug it on my computer (When I was 12 years old I would plug it fearless like there was no tomorrow, heh)