You imply teams don't currently place an emphasis on the conference meet and that's 100% wrong. There's a championship at stake and teams race their hearts out for it.
We're talking about the bubble teams here, not the top 40 or so schools. I'd wager that every athlete from a team "on the bubble" values winning a team championship MORE than being the 79th team in the regional they have no chance from advancing from.
Yes they'll still be happy to race at regionals but it's not like they weren't trying to win the conference until the implementation of an auto qualifer.