Apple disables True Tone and Auto Brightness regardless if the replacement an OEM or third-party. It's clear Apple simply wants parts pairing.
This might be a coincidence benefitial to Apple, however there is now a new problem with this approach that Apple might want to resolve sometime soon and which might resolve what you mentioned:
The part itself doesn't have a way to authenticate, pairing merely marks the serial number of the new part as genuine. The way Apple ensures that only genuine parts can be paired is by closely guarding their gsx pairing software. This has already been circumvented in two ways:
At first entire chips containing the serial number were pulled off the defective part and soldered onto the replacement part which worked but obviously required more effort. And now there's a device on the market that independent repair shops can purchase to reprogram the chip and copy the serial number from the defective Apple part to the replacement part in seconds.
Apple could use the serial number itself to encode the fact that it's an Apple part thus making pairing obsolete. This would then allow Apple parts to be accepted by iPhone automatically without pairing. However, I think what Apple ultimately wants to make sure is that iPhone cannot be spoofed into thinking it has an OEM part installed when it doesn't. And the serial number encoding won't prevent the copying.
So whatever they'll change next might very well include some sort of cryptography that actually authenticates the part properly instead of this terrible pairing that as you said also prevents genuine Apple parts from being accepted. That would then allow iPhone to identify parts as genuine without circumvention possible and it would do away with the need for pairing. Customers could know with certainty whether their part is Apple original or third party and original Apple parts could finally be swapped easily.
I completely agree with you that the way Apple does it now is terrible, but Apple has only really started experimenting with this on actual iPhone releases a couple years ago and I think what we have now is more of Apple making their first baby steps with parts authentication. Of course Apple should be criticized for this as it's now, my point is just that Apple might already know internally that their pairing isn't preventing third party apps to be spoofed to look like Apple original parts and if Apple is at all concerned with protecting their iPhone brand they'll overhaul this entirely.
Apple does get a lot of money from preventing use of other parts but from a security stand point the move may be good as mentioned in the article.
It's actually terrible from a security point of view. There is no parts authenticating and repair shops can now clone serial numbers from the original but defective part onto a third party replacement part. The pairing has thus been circumvented already and especially from a security point of view Apple should replace the current pairing process with their parts properly authenticating with iPhone. This would then make iPhone recognize original parts automatically without the insecure pairing mechanism and will both improve ease of repairs as well as well as security.