C'mon guys, is it really that bad??
In response to that, only when you don't know what to expect, and waste your time - such as thinking you have a valid pass to get you through security. If you knew what to expect, such as the machine saying "see an agent prior to going to security", or web check-in saying "you-a-screwed, get here early", it would be ok.
With respect to the reason for this procedure, I understand it completely, but know that the boarding agent could have a big "VERIFY COLLECT UG CERT" pop up on the screen or something similar when the seat # is entered/BP scanned, etc. If you're an SSSS victim, the agent sees that in a field taking up much of the screen when boarding.
In any event, it seems like much of this is short term problem/issue, and FWIW, people using these certs are entitled to use the F/MVP check-in lines.