Do snaps/flatpaks really not look at your local configs? Thats... terrible. I've avoided them already anyway because they seem like wholly unnecessary (and quite significant) bloat.
Flatpak does respect your GTK+ Theme - but you have to either have it installed in ~/.local/share/themes or youbhave to download your theme as flatpak package aswell. But that implies that someone has to maintain the flatpak packge.
While the most popular themes are available, more "niece" themes are missing. Do a `flatpak remote-ls flathub | grep --color "org.gtk.Gtk3theme"` to see all available themes.
Surely the sane thing to do security wise would be to mark each flatpak as needing config files foo and bar, and sticking those into the sandbox as well on launch. The app itself doesn't need filesystem access at runtime. Linux apps suddenly not reading standard config files on my system would be a pretty big downside.
I think part of the issue is that technically you cannot guarantee that config files written by the system-installed toolkit can be safely used by the flatpak-shipped toolkit. This said, I think flatpak actually makes an effort to use the ones available in the user’s home folder, whereas snap just does its own thing and screw everyone else.
They do by the way of an xsettingsdaemon (so not accessing directly) for security reasons. The obstacle instead is that they are self-contained, so they should not depend on the theme files outside their system. Hence, they will read what theme you are using and then inside their system look for a matching one.
While the most popular themes are available, more "niece" themes are missing. Do a `flatpak remote-ls flathub | grep --color "org.gtk.Gtk3theme"` to see all available themes.
Note: I'm maintaining a theme on flathub.