Thoughts on systems such as Naviance/Other Are they good indicators?

Yes, such things work better when a college does not admit by major or division and there are no specially preferred applicants from your high school.

A high school can partially mitigate that by maintaining separate data sets by major or division for applicable colleges where the number of applicants is large enough, and excluding the specially preferred applicants from the data sets. (But does any high school actually do this?)

Another data set that may be relevant to many is scholarships.