I don't think you added a new command line option. My suggestion was this:
Add a new command line option, say, --intel-cet (that's perhaps not the final name of the option, I chose it tentatively to move things forward.)
If --intel-cet is given, verify that each input file contains a .note section with an appropriate bit, and discard .note section after reading it (so we don't merge them or copy them to the output file). If there's a file that doesn't contain a proper .note, report an error and stop.
When creating an input file, create a .note section with appropriate contents when --intel-cet was given.
Specifically, I don't think you should add a new member X86Feature1AND to Config because with the above scheme you are no longer merging .note section so you don't need to collect bits. mergeAggregateMetadata should also be deleted from the patch.
