Do you have a specific example where they weigh the non con differently? They say they don't and I could see it being used to differentiate between 2 otherwise similar teams, but it'd take some effort to find something egregious that showed they do that.
Last year, Tennessee was #4 in NET and had the #2 Non-con SOS. They were 8-8 in Q1 and 4-3 in Q2. They were the #14 overall seed.
Kansas was #9 in net with a non-con SOS of 27. They were 17-8 in Q1 and 4-0 in Q2. They were the #3 overall seed.
Gonzaga was #6 net, #3 non-con SOS. 8-5 in Q1 and a Q3 loss. #10 overall seed.
UConn was #8 in Net, #16 in non-con SOS, 12-6, 7-1 and a Q3 loss and was the overall 13 seed.
UCLA was the 5ht overall seed with a 37 non-con SOS.
Purdue was #4 overall with an non-con of 89 and a Q4 loss.
Marquette was #8 seed with a NET of 12, non-con SOS of 160 and overall SOS of 54.
Kansas State was #11 overall with a NET of 24, SOS of 24 and non-con SOS of 163
Iowa State might get docked for its overall SOS, which is 62 currently and that is weighed down by a terrible non-con SOS, but there doesn't appear to be any indication that non-con SOS has any greater weight than the normal Q1/Q2 records.