Macbooks are abysmal for window management, for example. There are some lightweight tools that can manage some placement but they are neutered in one way or another. Deeper integration requires disabling BIOS-related security which I am personally uncomfortable doing, and still doesn't offer full control like you'd get on other Unix systems. Most of the OS is similarly untouchable.

Another example is Safari and its extensions ecosystem: an Apple license is required for publishing and as such even basic tools (stylus etc.) can require the user to purchase with no guarantee of developer support in the medium to long term.

OOTB the biggest example is the Mac-style hotkeys, its a persistent and extremely annoying problem for new Mac users and is, from the outset, unfixable via any sort of configuration, BIOS or not. Concretely: CTRL + T for new tab is now command + T, however switching tabs is still CTRL + Tab (Mac control is more like alt, in this case).

It's an eternal reminder that you are now stuck doing things the Apple way even if it's just relearning all of your hotkeys.