When I came back from Japan with a dog, I used GE in SFO and clicked the box on the screen for "Animals or Animal Products." Yep, it got me the "X" on the receipt as expected, but no one cared to examine my dog or her paperwork.

I expect picking up a dog off-site would work the same way; you'd get the "X" on the GE slip, and would just explain to the agents that you're picking your dog up off the airport grounds.