There is no problem, physically, with the location of the KTVU sites in TVFool.
Here's what is in the FCC's database. If you click on the listings in the table of your report, you'll get the path profiles used in the predictions. Note that the coordinates agree, and the main facility is on Sutro.
Note that the fill-in translator carries the same call-sign as the parent. That greatly complicates tracking its status beyond what is notoriously tricky to know already. The only error here is including the fill-in in the active list. There
is value in showing what's planned, as it may influence antenna choices.