Just reporting that I contacted Support and Mike replied showing me how to "Respect macOS Exclusions" inside packages. It is doubly tricky for folders inside packages! All the information needed is in the support pages.
Excluding items that exist within a bundle file
CCC "like TM" backups of Photos library, do recover as expected. I have tested that!
Mike strongly feels that macOS excludes too many things from TM backups and so does not make "Respect macOS Exclusions" the default. So this is a deliberate design decision. I accept the reasons for this, but will mostly continue to use the options to do exclusions like TM. Just glad, there is the choice.