Ok I figured it out. What wasn’t clear to me was that the --remove-signature has to be called on the individual bundles, and not the app itself.
So if anyone stumbles on this, what you need to do is :
codesign --remove-signature “APPPATH/Contents/PlugIns/resonanceaudio.bundle”
codesign --remove-signature “APPPATH/Contents/PlugIns/fmodstudio.bundle”
and then code sign your app.