The second part of the section 110.14(C)(1)(a) says: "Termination provisions of equipment for circuits marked for 14 AWG through 1 AWG conductors". Does that statement mean that any conductor from a 14 AWG to a 1 AWG shall be size according to the 60 degree C column even though the ampacity is greater then 100A?
Not necessarily. And the interesting thing about this rule, is that it is a lot more academic than practical.
If you continue reading this rule, you'll notice that it says "unless listed and labeled otherwise". It is the industry norm that most modern equipment is listed and labeled otherwise for using 75C rated conductor sizing in its terminations. However, if you intend to use the 75C rating, the burden of proof is on you and your equipment manufacturers, to have terminations/equipment on both sides of the circuit that are listed and labeled for 75C.
An unmarked terminal for 100A and less, is only rated for 60C.
An unmarked terminal for over 100A, is rated for 75C.
Most terminals and manufactured equipment you'll find in practice today, are rated for 75C.
It is common that you find terminals themselves as a stand-alone item to be marked for 90C. However, if part of manufactured equipment, you can't take credit for this unless the manufactured equipment is listed for 90C. This is rare.
It is also common that you find connectors that you'd separately install, to be rated for 90C. Given that you have this condition on both sides of the circuit, which is rare, you are permitted to take advantage of this, as long as it is separately installed, and not part of equipment with a limit on this rating.
The most common reason why you get to use the 90C rating of the wire, is for your ampacity adjustment factors and temperature correction factors. These do not apply to termination ampacities, but for the conductor ampacity once the termination rule is already satisfied. Consider two 60A circuits in a common conduit, such that there are 4 current-carrying conductors. The termination rating is 65A at 75C, and the adjusted 90C wire ampacity is 0.8*75A=60A. So the #6 wire in this example would be sufficient for a 60A circuit.
With Romex cable, there is an exception. It always has to be sized with the 60C column ampacity, even if terminals are listed/labeled for 75C, and even if the cable itself is listed/labeled for 90C.