Yes, I would agree the regions weren't evenly balanced. And I'm not giving San Francisco a full 5 points for being a conference champion, only unless they were ranked in the final poll, as well as one other team in their conference.
The conference title thing is the hardest to quantify, because it's impossibly subjective. But, still feel like it's important to include in the numbers. Kentucky, for example, would still be #1 on my all-time list, regardless of which conference they were affiliated with. But, they almost certainly wouldn't have that many conference championships if they played in the ACC.
San Francisco was still an elite team. They were frequently ranked in the top 10/20. In 1964 and 1965, USF lost to UCLA in the regional finals- and UCLA's smallest margin of victory came to USF both years.
So, would USF be ranked lower if they played in the East? Yes, almost certainly. But, I can't play what-if games and subjectively dock teams. Conferences have never been perfectly even. Tournament matchups have never been even. Just trying to find a formula that is uniform across the board, has multiple metrics, and minimizes the errors as much as possible.