org.glimpse_editor.Glimpse does not set Flatpak GTK theme when choosing the Preferences > Theme > System option. I am currently using the org.gtk.Gtk3theme.Plata-Noir theme.
Steps to reproduce the behavior:
It should look like this (Taken from GIMP)

It should look like the picture above ^

I will need help for this.
Seems like org.gimp.GIMP also has this problem.
cc @TrechNex this doesn't seem like a too pressing issue, but just in case, I'll cc @bochecha in.
Do note that Glimpse (and by extension upstream) uses GTK 2, which might not play well with GTK 3 themes.
The issue is most likely due to the flatpak sandbox; though. Which is (again) bochecha's area of expertise.
The issue is most likely due to the flatpak sandbox; though. Which is (again) bochecha's area of expertise.
It works with any other Flatpak programs (should've said that before).
Hence, i cc'd bochecha in. He's the person who's been mainly responsible for the flatpak manifest, so he should know how to get it to work. Since it works on other flatpak applications I'll mark this as a bug.
In theory you've done the correct thing. I use the Snap version as my daily driver and setting "System" UI theme in Edit > Preferences > Theme works for me on Ubuntu 18.04 LTS.
I just tried on the built-from-source version and the System theme looks entirely different. Let's take some time to see what the Snap does that's different and see if we can replicate it for Flatpaks, etc.
@Member1221 is correct that we inherited GTK2 code and a custom theme engine, so we should also review if upstream have fixed this problem in 2.10.18 which we'll eventually rebase to anyway.
Just spotted part of original post that says it doesn't work for the upstream code either.
I'm categorizing it as a "fork candidate". If we can find the time to troubleshoot this then brilliant.
Worst case scenario, it may have to wait until upstream release v3.0 (which will be based on GTK3) and then rebase to it. But hopefully we can produce a solution much quicker than that :)