Tbh, for me the value of flatpak is in the isolation (great for how easy it is to achieve), rather than the compatibility.
For example, I run obsidian with no network access and fs access to just the path where my notes are stored. This is really reassuring considering I am not really sure what all the plugins might do. While it is not perfect, it’s much better than having it running natively in my box (I.e. root namespaces).