The common shortcuts do work in 99% of situations. The primary exception is terminals.

The problem is mainly that Linux has two clipboards running simultaneously, with slightly different behaviors.

In reality, the clipboard works fine. There are some gotchas, but for everyday use it's perfectly fine. The opinion expressed by parent comment is, uh, unconventional. I've never heard this take before. Most people consider Linux clipboards an annoyance that we should fix someday, it's not a showstopper by any means (for average users)

I like them being separate. The main one feels more intentional than the selection buffer, which I mostly use for grabbing text I want right now. I'd be annoyed if my main clipboard got overwritten every time I selected text.

I just tend to completely forget the select-clipboard even exists - right until a HN submission reminds me, or I drop some garbage in the middle of the text I'm writing.

Text-wise the only thing I can think of where clipboards don't Just Work is indeed terminals, but I hardly consider that an issue in practice. Either it's a trivial session and I'll happily right-click to paste, or I'm in tmux and using lead key prefixes for shortcuts already.

Cross-app rich media copy/paste does have a habit of being a bit buggy from time to time, though...

In practice, it's not really an issue. In some applications (most notably terminal emulators, where ctrl+c is already used to terminate a process) you have to use an alternative combination (e.g. ctrl+shift+c).

MacOS neatly avoids this issue with the command key, but I'm not sure what happens in Windows.