Sometime the concept is a bit difficult to understand. You need to recognize there is a difference in a conductors ampacity and the rating of the branch circuit. Ampacity is the current a conductor can carry without exceeding it's temperature rating. For the most part it's related to the type insulation and the current allowed without causing damage to the insulation. A #10 THHN can safely carry 40 amps continuously without damage to the insulation whereas the same conductor (#10) with a TW insulation would suffer damage. So your adjustment factors (fill, ambient, etc. take into account factors that can increase the temperature the insulation encounters (more wires in aconduit the hotter temperature the insulation encounters)
The second part of your post addresses Art 240 which is the overcurrent device which determines the circuit size. It is direct;y related to ampacity but takes into account termination temperatures as Dennis notes (110.14) and other factors. 240.4 is a guideline for selecting overcurrent devices to protect the conductor (and, at times, the utilization equipment) in accordance with it's ampacity. 240.4(E) & (G) address situations where those "general" rules in 240 need to be altered due to circumstances particular to those specific situations (motors, HVAC, etc),.