TestFlight uses a device enrollment challenge to get your device identifier, not native code. There's no native code in TestFlight - that's why it's not in the App Store and hence can't get rejected. It's just a clever use of Apple's remote provisioning capabilities (originally designed for enterprise customers).

So this change both can't and won't kill TestFlight - the only way Apple could kill TestFlight would be to change the way their enterprise provisioning and OTA installation process works, which they have no incentive to do as the process requires very explicit user permission, isn't being probed by lawmakers, and makes them that much more attractive to enterprises.