This will be a bit of nit picking, but I never liked those little bugs anyway. :roll:
If we keep to an ambient temperature of 30C and limit the number of conductors to three, then the "ampacity" of a #14 THHN is 25 amps. Nothing else in the code changes that. While it is true that we must use a 15 amp breaker for most applications of a #14 wire, what we are doing in those cases is protecting a wire with an ampacity of 25, using a breaker that is rated at 15 amps.
Keep in mind that you don't get to article 240.4(D), without first going through article 240.4. The basic rule is that we must protect all conductors at their ampacity, unless otherwise permitted or required by the subsequent paragraphs. Therefore, what 240.4(D) does is to require us to protect certain wires at values that are below their ampacity.
Article 110.14(C) works in a similar fashion. The ampacity of a #12 THHN is 30 amps. But we must protect it at a value that is lower than that ampacity because of terminal limitations.