Interesting thing is that this really doesn't matter for any conference except the Ivy which has yet to implement a conf. tournament (they are talking about it,) For everyone else they just half to get hot for three for or five games of their tournament to get the auto-bid.
While that is true - and I haven't heard much lately of discussions to eliminate tourneys - conference championships are a prize all their own. Teams can certainly tout them, even if they are (unfortunately for them) upset in the conference tourney. In most of the lesser conferences, it doesn't often happen. But if you look at the Horizon, for example, the 2 front runners might be matched up again in the tourney championship.
What regular season championships do accomplish is get you bids to the WNIT, which for some of these schools can be important, if you lose out on the big dance.