[lld-macho] Don't warn on non-existent system libraries

Now, new mach-o lld no longer warns if the isysroot has just
usr/lib and System/Library/Frameworks but is missing usr/local/lib
and System/Frameworks.

This matches ld64 and old mach-o lld and fixes a regression from D85992.

It also fixes the only test failure in `check-lld` when running it
on an M1 Mac.

Differential Revision: https://reviews.llvm.org/D91891