But the problem does exist, right?
Not really. It's more a
user problem: you're used to the behaviours of other OSs and find yourself a little "lost" in Linux. Other people (like, say, I myself) are more used to the "normal" Linux behaviour (if there is such a thing) and would find strange if Lazarus behaved otherwise.
For example, first thing I do after an initial install of Lazarus on Linux is to change a lot of the hotkeys to Linux's "standard": Ctrl+W to close an editor Window, and so on, because a lot of the default hotkeys (with Ctrl+, Alt+ some function key) are usually taken already by the Window Manager to change workareas, virtual screen, or whatever. For similar reasons, our default Linux application template has a FileExit action associated to Ctrl+Q, etc.
In the end it's a question of expectations, and the proper (or conventional) thing to do is to follow the platform rules as close as possible, even such "loose" rules as Linux has, not try to mimic in one system the behaviour of another.
IMHO, of course