[Ferk]

The problem with combos is that not all controllers have the same buttons. Genesis controllers are missing a Select key. Some controllers are missing shoulder buttons or triggers. The gamecube controller has two triggers but only 1 shoulder button, for example. This means we can't show button names in the GUI, and documentation will always need a long explanation of logical vs. physical controller mappings. etc.

You are referencing controller schemes from consoles. Isn't retroplayer using the retropad?
The retropad does have select and start buttons that can be bound to a physical gamepad or even a keyboard.

It shouldn't be a problem if Genesis, N64 or MAME have weird control schemes, at least in Retroarch, because the cores do not really read input from Genesis or N64 but from the libretro retropad. Some N64 cores even use some input hacks (like having one shoulderpad act as "meta" modifier) to simulate the N64 input with the retropad.

Maybe the problem would be more about the physical controller the user is connecting to their kodi device, if it does not have enough buttons to bind them to the retropad. In this case the "holdtime" for "Start" might have an advantage vs the button combination (as long as "Start" can be bound to the physical gamepad).
Though, imho, maybe that case is not one that retroplayer should care that much about. If a user has a physical controller that cannot fully support all the functions retroplayer can offer, users could either edit the config to match their gamepad, use an alternative (IR?) control or get a gamepad with more buttons.

In RetroArch, if select is used as a combo button, how do you send a select press to the game? If you press Select + L1, does the select press also get sent to the game?

That's a good question. I expect it doesn't send the Select+L1 buttons when they are detected, but if you don't press them exactly at the same time it probably does set either Select or L1 (whichever was pressed first) during the instant of time that one was pressed before the second one was.
I would have to test that. I think most games I've played do not really use Select much, outside of menus, so I wouldn't have noticed.