Stupid question about flatpak

Sorry for the newbie question, but is it ok to have the same program installed from the repository AND flatpak at the same time? Or is that going to give me trouble?
Does flatpak save application settings in the same location as repo applications or does it have its own location?

There are no dumb questions.
No, you won’t get any problems, because the Flatpak programs run in a kind of Sandox.

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