So, it is a dilemma. According to 310.15(A)(2) one may take the higher ampacity into consideration if the conduit is less than 10 ft. or 10%.On the other hand according to 110.14 Electrical Connections. (C) Temperature Limitations.[Less than 100 A load 60oC and for more 75oC.]
?Unless the equipment is listed and marked otherwise?. You have to be Smart.
The termination rule trumps all other sizing rules. Even though a termination is obviously less than 10 ft / 10% of the remaining length.
For what it is worth, most of the terminals you find on new equipment today are "listed and labeled otherwise" for 75C. It is more of an academic rule to have 60C being the default. It is very rare that you have terminations AND EQUIPMENT rated for 90C. Field-installed terminations, separate from manufactured equipment, can take credit for the 90C rating. Examples are MC4 connectors, Polaris insulated tap connectors, insulation piercers, and similar.
For your conduit of wiring emerging from equipment to cable tray, there are two rules you can likely take credit for, in order to ignore the bundling derates in the conduit:
1. the 24 inches and less "nipple rule". No derates need to apply for conductors this short.
2. the less than 10%/10ft of remaining length, "stub rule" as discussed above.
Note that the NEC is silent on how to calculate cable tray conductor ampacity.