you still can't have multiple windows with flutter, which disqualifies it for building desktop apps.

True. But this is actively being worked on by Canonical: https://ubuntu.com/blog/multiple-window-flutter-desktop

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How exactly is it a problem for the typical desktop app?

There is an unfortunate increasing trend to build desktop apps that only live in one window, so it's not really a "disqualification" - perhaps more a "complication".