I'm gonna say "no" to San Fran. They are just less bad than the rest, but they're not a good team. They haven't played anybody outside of Gonzaga and St Mary's, and they're 0-4 in those games. They wouldn't finish in the top 2/3 of any major conference. They'd probably finish dead last or near last in just about every P5 conference. KenPom has some uses, but it's highly deceiving when teams have a bunch of wins against below average teams. ISU was at or near the top in KenPom at one point this season, now they're near the bottom of the Big XII, after they finally started playing some competition.
Good on Santa Clara, but TCU early in the season is not the same as they are now. For one, they were missing two of their starters in that game, and they also were a team with a lot of new pieces who were trying to figure out how to play together. They've been very inconsistent for most of the year, but the light is starting to come together. They have some very good athletes but struggle with shooting and ball security. A bunch of individual pieces that didn't know how to play as a team. They're starting to figure it out though, and I'd hate to face them in the 2nd round as a 1 or 2 seed. But early on in the season they were not good. That same Santa Clara team lost to UC Irvine, Louisiana Tech, Boise State, Fresno State, and California(the 2nd worst team in the PAC). If the two teams played now, I'd lay HEAVY money on TCU to win by a large margin.
BYU? Again, you're going to struggle to convince me that a team that lost to Utah Valley, Creighton, and Vanderbilt(near the bottom of the SEC) is good. No, they aren't terrible, but they are still a team that any top 10 team should expect to beat easily. Yes, BYU did have a weird win over Oregon, but that's kind of the schtick of the PAC 12, a bunch of athletic teams that are extremely bi-polar. They'll come out and beat a top 10 team one night and lose by 20 to a bad team the next.
Regarding their Quad 1 wins, sure. But there are Quad 1 wins and then there are Quad 1 wins. Some teams play a bunch of Quad 1 teams that are near the top of the Quad and other teams play a bunch of Quad 1 teams that are flirting with Quad 2. Gonzaga usually plays a couple games against those Quad 1 teams near the top, and a bunch of teams that are borderline Quad 2.
All of that being said, Gonzaga is a very good team and I do believe they're a legit top 5 team. But the arguments that their schedule isn't that bad are not great arguments. They're a very good team that plays a shit schedule. They do try to make up for it in the noncon, but they can't really make up for their conference schedule by playing a couple good teams in the noncon.