[Haemm0r]

You don't need Flatpak at all to have these kind of usability issues, it is deeper than that: For example, if you mount a samba share in the Linux Mint Cinnamon file explorer it is just good to use it from there. Accessing files from the mounted share from "external" apps is a pita (shares are mounted to some obscure path(permission issues), the apps filepickers never have the information that a share was mounted, etc.). If you want usesful access to a samba share you have to mount it via terminal; This way at least the path to the share is short.

[skydhash]

I think that because a lot of gtk apps use gvfs[0]. And most kde apps use kio[1]. But if you want files access through the standard syscall. You have to use the standard mount program or fuse.

0: https://en.wikipedia.org/wiki/GVfs

1: https://en.wikipedia.org/wiki/KIO