Since SuperDuper, etc. cannot
write the com.apple.rootless Extended Attribute that marks the files in question, it will drop that Extended Attribute in the copying process. Therefore the clone it creates will not possess "System Integrity Protection." After restoring from a clone, the workaround is to reinstall the OS, which will overwrite the vulnerable files with the com.apple.rootless Extended Attribute.
It's all there in
Shirt Pocket Watch - Uncovering our rootlessness.
