As far as the multiple BP checks, yes they are a pain but they actually do serve some sort of a purpose. It is not just about double checking for SSSS. At my airport, our checkpoints are roped off with stanchions. Some people will try to bypass the initial BP/ID check by ducking under the ropes and butting in line for the WTMD. I have had people without boarding passes do this, and they get caught at the WTMD. If we only did a BP/ID check at the WTMD this would really hold up the lines.
But it is not consistent - there are many airports that do not examine the BP post-WTMD. I had a theory that this only happens at airports with dedicated haraSSSSment lanes. For example, SJC has common lanes, so those with haraSSSSment are flagged post-WTMD. IND has a dedicated lane, where you are directed once the ID checker notes the haraSSSSment.