Did the DR actually change? What does it look like if you dump the DR of your old appex and the DR of your new sysex?
I believe this clued me in on the reason. The issue is that when we create a configuration profile in our app, it takes the designated requirement of that app. We would then install a TestFlight build, and that would have a different designated requirement. Since it's signed by the TestFlight signing cert vs the App Store signing cert.
I was able to verify that a configuration profile created in a TestFlight app extension build would work on a TestFlight system extension build, since their DRs would be the same for both.
But a profile created on an AppStore build would not work on a TestFlight build.
I obviously can't verify from AppStore -> AppStore easily. But I believe that the fact that this works TestFlight -> TestFlight proves the hypothesis.