Just like the old RPI, you are going to have some outliers. However, I have no answer in regards to Colgate or how they are at 11. At least Loyola is #10 in Kenpom, primarily because they are #1 in defensive efficiency in the country.
As Wichita said, outside of the "quads" classification setup, this metric also has built-in variables like scoring margin, location, and efficiencies. Loyola may be robust in a couple of these advanced analytics, but they won't get anything higher than a 7 or 8 seed....simply because they won't have the resume (they only have one quad-1 win, but they are 4-2 in quad-2 games).
I know that the committee looks at several ratings system, but uses NET as their main "advanced metric". Again, I'm sorry I can't give you a better answer.