The code signature is on the multiple architecture binary, thereby including any statically linked object files, right?
If Apple were to add dynamic libs, they would presumably be separate binary files, with their own signatures. This could raise the concern noted by 0x0.
Separate binary files have individual hashes, which are included in the package manifest file. The manifest is then signed, so a single signature covers all hashed files in the manifest.
Curiously though, in all of the MAS apps I've checked, bundled dylibs are explicitly not hashed in the manifest. This is the developers choice, but perhaps a default?
If Apple were to add dynamic libs, they would presumably be separate binary files, with their own signatures. This could raise the concern noted by 0x0.