But the NCAA does not force a conference to hold a championship game / tournament.IIRC Our conference would prefer to recognize the regular season champ but are forced by the NCAA to select the tournament champion. The regular season champ is a much better indicator of the respective strengths of the individual teams due to the number of games played. Football doesn't have that.
Also what happens in the final few weeks of the NFL is not indicative because many teams who have achieved the highest seeding they are able to attain (whether it be a wild card, home team throughout, or somewhere in between) often, very often, rest their starters by only playing them in a quarter or a half.
In basketball, Frank McGuire argued against the ACC holding an end-of-season tournament to determine who would represent the league in the dance, for the reasons you indicated.
To McGuire's credit, he was consistent in his opposition to it, both while at UnCarolina and at USC. As we all so well know, it finally caught up with him at the 1970 ACC Tournament.