File type associations are not maintained by GNOME: GNOME consumes the data in the shared-mime-info database.
It’s entirely possible that FreeCAD is shipping its own extensions to that database, which is allowed; but AppImage is a self-contained distribution format that does not interact with the system in any way (which is why it does not provide desktop files either, and requires manual installation of files by the user), so it’s unlikely that it’ll work for MIME type extensions, or icons.
My strong recommendation is to stop shipping AppImages, unless you’re also willing to document how to integrate them into a freedesktop system, something that the AppImage development community is wholly uninterested in doing, seeing as they are trying to replicate the macOS app deployment mechanism.