> Modals that blocks focus to an entire browser window aren't really a good idea (I'm of the opinion that they are almost always a shitty idea, but that's harder to argue).

Good news then, because alert/prompt/confirm do not block the window in any modern browser!

In Firefox it only blocks the viewport of the current tab, so it behaves exactly like a DIY modal. In Chromium browsers it does pop over part of the browser UI, but it still doesn't block the window; You interact with the tab bar, address bar, menu, etc.