Some additional info: I have found that it is removing Full Disk Access completely. Before I was leaving the versions the same for all .pkgs when building, and now I am incrementing by one, and I see the same error but Full Disk Access is actually getting removed. It is truly removing full disk access, but I'm not sure why, it should be a standard installation which should not cause it to be removed.
I've also tried installing the binary to a separate location and changing the .pkg identifier for that step, and it still removes Full Disk Access, suggesting maybe something to do with a rollback of the previous package?