For example, currently, if --enable-archs=i386,x86_64 is used, and there is an
x86_64 cross compiler present but no i386 cross compiler, Wine will silently
remove i386 from the list of cross-compiled architechtures, and only compile
PE code for x86_64. This seems quite undesirable.

I am not aware of any practical reason for this to happen. Debian does ship
i686 and x86_64 MinGW compilers in separate packages, though, so it is possible
in theory.