First, to take care of the factual errors in your post. Atlantic Hockey has not only had a realistic shot at an at large bid, they've received one when Niagara failed to win the conference tournament in 2013 yet received a 3 seed in that year's NCAA tournament. Air Force's 2017 squad just two tournaments ago was also seeded 3rd and likely would have received an at large bid had they lost the conference's championship game (this despite the fact that they did not even win that year's regular season title in Atlantic Hockey, which is a testament to how much the AHA's teams beat up on each other). In fact, in 2017 the WCHA winner was the 16th overall seed (27th in pairwise) while Air Force was ranked 12th in pairwise. The 2017 season is also the only season in the past 3 where the 16 overall seed did not topple the top seed.
Secondly, it's not nearly as silly as you claim. There's a legitimate question to be asked here. A conference's strength is not just measured by the teams at the top, it's also measured by the team's in the middle and the bottom of the conference, and the latter is where Atlantic Hockey has made significant strides over the last few seasons, while certain teams in the WCHA seem to be hurting from the after effects of the realignment that happened a few years ago. Right now, I don't think there's any doubt whatsoever that the bottom of Atlantic Hockey is better than the bottom of the WCHA. And while yes, it's almost certainly true that Minnesota State is better than the top of Atlantic Hockey (NCAA failures notwithstanding, including, I might add, a loss to RIT), their overall record is also benefited from having to play teams like Alabama-Huntsville and Alaska twice a year each. Meanwhile, the team that finished in last place in the AHA this year swept North Dakota (one of the few times a big program has agreed to visit an AHA team's home barn for two).
The two conferences H2H records are fairly close over the last 3 seasons, with the AHA actually holding a 10-8-2 advantage, and the overall non-conference records are fairly similar over those 3 years combined:
AHA: 51-125-23 (.314)
WCHA: 56-122-17 (.331)
When you add in playoff games into those records, the records get even closer (the AHA is 3-3-0 over the past 3 years, while WCHA is 0-5-0), and the last matchup in the tournament between the conferences was the aforementioned RIT upset of Minnesota State.
TL;DR version: Yes, the top of the WCHA is almost certainly better than the top of Atlantic Hockey. But I see no evidence that as a whole conference that the WCHA is any better than Atlantic Hockey, and the AHA is clearly stronger at the bottom of the league now that teams that have long been cellar dwellers (*cough* *cough* AIC) have made a renewed commitment to their hockey program.