Simplify module flags copying and defaults handling (#61749)

Both `OverrideStackAlignment` and `getStackProtectorGuard` are
ModuleFlags and should already be copied over, but
`m->setStackProtectorGuard(source->getStackProtectorGuard());` will set
the stack-protector flag to be the empty string.

Instead, we can copy the flags over from the source and then if they are
missing, initialize them to the expected ones.