I don't have Obsidian around, but this has been happening elsewhere lately too, almost certainly because of this underlying Electron issue: https://github.com/electron/electron/issues/43819

Unfortunately there's not much you can do about it. Electron decided to depend on functionality not yet in a released version, and that very interesting choice flows down to everything that updates their Electron on the regular.

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my flatpak knowledge is malnourished; but looking at it from a high level containerization perspective, i would presume it depends on it the file system overlay is setup.

normally something like that would be defined in either the source image of the container or the mechanism used to modify that source image (eg dockerfile). if it's the latter it will be in the project's source and that source is probably on github. you should be able to search for terms in that source like "docker create" or "podman compose" to see how it's configured and use that has a starting point to search on something like google or openai.

this isn't an easy answer and i can go into lower level details; but your post contains a few key words like plasma and xdg-desktop-portal that says to me that you'll be able to figure it out how to make my advice actionable for your own specific situation if you think it applies and i hope that this lead pans out for you.