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Drag and Drop is an absolute mess
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It's not as black and white as they say. Flatpak is not a bad choice per se but not without tradeoffs and they can come with catches like this because of the security model. There is no one-size-fits-everyone here. If you want all your apps to have access to everything your user does and value convenience over the sandboxing, flatpaks might not be the best choice for your situation. Also like for any repo with external third-party uploads, quality varies a lot between apps and maintainers on flathub. Some are excellent and some are in a sorry state. Before installing from fllathub its a good idea to some basic due diligence on the package and maintainer before jumping in.
I agree with the IanTwenty that the UX has room for improvement in making it more obvious what's going on and making it easier to manage customizations and overrides. For the time being, getting comfortable with Flatseal and learning more about Flatpaks seems like the best way for a user to make it work for them if defaults don't work out.
Flatpak has tradeoffs and whatever is on flathub is not guaranteed to always be your best pick. That doesn't make it Bad. Going as far as calling them harmful in general is hyperbole. It can still be a great option for many users.