Best to abandon the default keys now rather than them causing issues again and again in the future.
do the default keys normally cause issues?
The oddball keys like ctrl, alt, shift can't be used on some of the console emulators.
I don't recall which ones. We should have compiled a list of them long ago.
People usually end up using an alternative emulator.
There's also the issue of posting windows hotkey commands during gameplay.
The one that usually gets people is CTRL+ALT+Arrow which rotates the desktop.

Luckily hotkeys can be disabled.
I don't know why people cling to the default keys. I guess they're using an x-arcade cp or downloading the stuff pre-configured for the defaults.
IMO, the only time it really makes sense to stick with them is if you're using an inferior keyboard encoder that has a low limited number of simultaneous presses.
The oddball keys usually don't count toward the limitation.
(YouR JPAC doesn't have that limitation)
The reason you haven't seen anyone warn against the default keys is that a lot of people don't venture too far from MAME.
They don't install all this other stuff, so the default keys are never an issue for them.