Recent TSA Gate searches I've experienced at MDW and CMH have both occurred while boarding was in progress. The TSA agents selected two BS pax who were pulled out of line while the rest of the A 1-30 line boarded ahead of them. They essentially lost one of the main benefits of the BS fare.
I was A-17 a couple days ago at MDW and was selected by the TSA Agent while the boarding line was moving in front of me. I stopped where I was at and put my arms and legs out for the pat down as instructed. As a taller guy, I benefited since my arm/leg span blocked the line behind me making me difficult to pass. Had this not been the case, my A-List status benefit would have been lost and I would have probably boarded somewhere in the A 31-60 range.
WN needs to coordinate these gate screenings with the TSA to ensure it does not disrupt boarding order, especially those on BS fares. Either have these occur prior to boarding altogether or have the GAs hold boarding at the end of each group (A-15, A-30, A-60, B-30, B-60) to allow passengers who were pulled out of line and screened to board before the next group.