The specification does, in fact, apply to the wires within the connection box.
When UL tests a fixture, temperature measurements are an important part of the testing. Where there might be a problem, UL will require that wires in the area be of a certain insulation, the fixture be marked "Not for use inside residences," etc.
Ordinary THHN qualifies as 90 degree wire, so there's not a problem. What do you do if the requirement is for, say, 105 degree wire? Well, you end up having another j-box a couple feet away, and running the expensive hi-temp wire those last few feet.