A new post on the TSA blog gets the logic behind the strip/grope combination correct.
[I]f you’re selected for AIT and choose to opt-out, we still need to check you for non-metallic threats. That’s why a pat-down is required. If you refuse both, you can’t fly.
Any alternative allows someone concealing something to decline the strip-search machine, decline the intimate pat-down, and leave the airport, returning another day in hopes of not being selected for the strip-search machine. The TSA reserves the right to fine you $11,000 for declining these searches.
So the question is joined: Should the TSA be able to condition air travel on you permitting someone to look at or touch your genitals?
I've argued that the strip/grope is security excess not validated by risk management. It's akin to a regulation that fails the "arbitrary and capricious" standard in adminstrative law. But the TSA is not so constrained.