Flatpak package contains files only required at build time

The current Signal flatpak (version 8.2.0) contains files that _I think_ shouldn't be there, for example:
* `/app/org.signal.Signal/current/active/files/bin/gvfs-trash`: This just makes `gvfs-trash` into `rm -r`, which seems wrong. I think whatever need this file was there for might be gone. Source: https://github.com/flathub/org.electronjs.Electron2.BaseApp/blob/1220f81c64db460092614d4cc27c6dac0a56e2a9/org.electronjs.Electron2.BaseApp.yml#L51-L60
* `/app/org.signal.Signal/current/active/files/bin/patch-desktop-filename`: This is part of the build system, shouldn't be in the package. Source: https://github.com/flathub/org.electronjs.Electron2.BaseApp/blob/1220f81c64db460092614d4cc27c6dac0a56e2a9/org.electronjs.Electron2.BaseApp.yml#L92-L99
* Under `/app/org.signal.Signal/current/active/files/lib/python3.13`: python package `asar` for `patch-desktop-filename` above. Source: https://github.com/flathub/org.electronjs.Electron2.BaseApp/blob/1220f81c64db460092614d4cc27c6dac0a56e2a9/org.electronjs.Electron2.BaseApp.yml#L79-L91

At least the second and third item, maybe also the first one, are only needed at build time, i.e., when the package is being created. However, they are not needed at runtime, so they (ideally) shouldn't be part of the flatpak package.

Is there any way to make these files available to the build system without copying them into the resulting package? Or, as a workaround, to copy them into the package, but remove them before the package is finalized?