I was at WDW last week and also used TP Lines app. The TP predictions that were shorter than the posted wait time were not always correct. We got in line for Flight of Passage and the posted wait time was 55 minutes and TP said something like 35 or 40. We definitely waited 60 minutes in line (I used the TP timer and submitted). So it just depends.
I don't know if this has any bearing on the official posted waits, but with social distancing the lines stretch out much farther. At the parks, they seem to indicate that the line will take such and such minutes from a particular spot. Now, if that is based on people using the "wait here" markers through the whole line, then those estimates based on distance may be very off depending on how well people are observing the "wait here" markers. I saw many examples of where a whole length of a back and forth queue section was supposed to be empty according to the distancing markers, but it was full of people just like old times. I wonder how that kind of thing throws off their wait time estimates.