I want to keep some applications running so it continue to receive its own thing in the background, but I do not want to accidentally open the window during Alt-Tab, e.g. my email client, my chat application. (On macOS it's still showing up on Cmd+Tab, but selecting the application doesn't activate the window).

I think this design decision still makes sense in 2022. On Windows and Linux, applications can have no window open by installing a background service (ugh) or hide to status bar, but application need to explicitly implement the behavior. On macOS, this is the expected behavior.