I'm not entirely sure of your point. St. Mary's is barely in the tourney, but they do have good wins against BYU and Creighton. Teams like St. Mary's play the schedule they can, to a certain extent. Often, that means they won't get at-large bids for just the reasons you outline above; they can't get games they can win against good, but not great competition. But this year, while they didn't have great wins, they frickin' pounded the teams they were able to beat. Kind of a mini-Florida scenario.
My hope is that St. Mary's is in because of a growing trend to using better analytical tools (e.g., they're kenpom 22) and they pass something of the eye-test and have a good win or two and didn't lose any true stinkers.