I have figured this out: The provisioning tool creates a file called signed_sb.bd, and inside that file there is a line that says
"erase all"
You can changed that to
erase 0x0000..0x3C600;
and just that range will be erased. But, when you run the provisioning tool "build image" again, it will revert to the "erase all" which can confuse things.
Another point of confusion is that if you specify an axf for the provisioning tool input, it appears to silently convert it to a bin and move it to a new directory and that step won't be captured in the scripts. So, the end result if you specify an axf for input is that the tool works, but the scripts don't. The solution is to force a bin in mcuxpresso via post build step, and then use that bin in the provisioning tool. Then the script works.
One last note of caution to myself: Just exporting the keys to a safe location doesn't seem to be everything you need in the event of a disaster. You also need the SBKEK.
Clarification on the manual discrepancy noted previously would be appreciated. Thanks