@Ludvig nice to see you're getting this ready for Flathub! Since I just went through this with DarkRadiant, I took a look at your manifest to see if there's anything that will trip up the process:
Comments are fine, but they don't like commented out lines so you'll want to clean those up before submitting.
They require a 64x64 and a 128x128 icon file, and the one you're providing is 48x48. You might need to go hunting in the assets or on the wiki, or see if someone here has a suitable icon lying around.
I'm not sure about having --socket=wayland and --socket=x11 together. If we don't have explicit wayland support then --socket=x11 should be sufficient on its own; if we do, then I think you use --socket=wayland with --socket=x11-fallback.
You have --talk-name=org.freedesktop.Notifications but I don't remember anything in TDM or the installer that would make use of it. If there is, feel free to correct me
You'll need a flathub.json file that tells their build system which CPU architectures to support or skip. Without this, I think it will try to make an ARM package too.
Once you've got an appstream file I'll gladly check it over for you too.