Yes, the terminations come into play in the big picture, however, you're incorrect that 50A circuits require #6.
You are correct in that the code tells you that by default, the 60 deg C rating is to be used. However, your blanket statement that the temperature rating is always 60 deg C for less than 100A is incorrect - 110.14(C)(1)(a)(3) notes the following may be used: "conductors with higher temperature ratings if the equipment is listed and identified for use with such conductors"... every breaker and receptacle I have on my workbench today is listed for 75 deg C, and I have a sampling of types and brands. The ampacity of #8 wire at 75 deg C is 50A.
There are two cases, though, when you must use the 60 deg C column, and they're specified by articles 334 and 338, where NM and SE cable are used for branch circuits - the 60 deg C column must be used for those cable types.
As a result, you only need #6 when you're using NM and SE cable assemblies, but THHN/THWN wire in conduit is fine at #8 for 50A.