As stated in the title, the flatpak'ed version of Geany 1.33 does not properly inherit the GTK theme as the native, non-sandboxed version of the application does. 
The Geany project doesn't make flatpacks, we make the non-sandboxed native version (the one that works :grin:). You are more likely to get help if you post to the source of the flatpack.
Whoops! Thanks for pointing that out, I'll file an issue over in the appropriate flathub repo in that case!
Closed #1917.
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