...whose idea it was to have shortcuts differ by OS??

It is not uncommon at all? A lot of programs have slightly (or majorly) different shortcuts in windows vs linux vs macos. There are usually differences in the keyboard layouts themselves (command key in macos, super key in linux, windows(?) key in windows), as well as in system shortcuts generally.

If in most linux distributions ctrl+. opens the emoji pickers, it is not weird that they implemented it there, and not in other OSes where it would not make sense.

I think it's more that no one tried to align shortcuts across OSes, and it'd also be a huge endeavor and to be honest, sounds like it wouldn't be worth it. Takes a couple of seconds to adjust and orient yourself even if you switch between Linux, Windows and macOS multiple times per day.