Even if I-540 didn't connect two interstates (i.e. if US 64 were never made into I-495 or I-87), it should still have been designated I-640 and NC 640 since it's a beltway, even if not all of it is an Interstate. It was clearly originally meant to be entirely Interstate before the toll road option was chosen, and I believe the plan is to remove the tolls when the road is paid off decades from now, so in that case then it will be able to be all-Interstate one day. I have no idea what they were thinking when they planned the number, since I-640 is still available and as far as I know was never planned to be used anywhere else.
That being said, as dlsterner said, they shouldn't change it now after the fact just to satisfy roadgeek OCD. Even decades from now when/if the tolls are removed and it's all eligible to become an Interstate, I wouldn't mind just making it all I-540, even though AASHTO would likely object.