TransformUtils: Fix metadata handling in CloneModule (and improve CloneFunctionInto)

This commit fixes how metadata is handled in CloneModule to be sound,
and improves how it's handled in CloneFunctionInto (although the latter
is still awkward when called within a module).

Ruiling Song pointed out in PR48841 that CloneModule was changed to
unsoundly use the RF_ReuseAndMutateDistinctMDs flag (renamed in
fa35c1f8 for clarity). This flag papered
over a crash caused by other various changes made to CloneFunctionInto
over the past few years that made it unsound to use cloning between
different modules.

(This commit partially addresses PR48841, fixing the repro from
preprocessed source but not textual IR. MDNodeMapper::mapDistinctNode
became unsound in df763188 and this
commit does not address that regression.)

RF_ReuseAndMutateDistinctMDs is designed for the IRMover to use,
avoiding unnecessary clones of all referenced metadata when linking
bet...