[clang][deps] Ensure module invocation can be serialized

When reseting modular options, propagate the values from certain options
that have ImpliedBy relations instead of setting to the default. Also,
verify in clang-scan-deps that the command line produced round trips
exactly.

Ideally we would automatically derive the set of options that need this
kind of propagation, but for now there aren't very many impacted.

rdar://105148590

Differential Revision: https://reviews.llvm.org/D143446