Darcy -- Is the laptop section held to the rest of the bag by the new connectors that allow for the removable waist straps? That's a *great* idea. It's semi-permanently attached to the rest of the bag, but it's also possible to remove the laptop section by itself if necessary. I love those little Tom Bihn touches!
Just unfold your Checkpoint Flyer and place it on the conveyor belt. If somebody reminds you to "Remove all laptops," just ignore them, or nod and say, "I'm good."
The people checking the scanner are the ones who know what to look for, and the only reason they should ask you to remove your laptop from the bag is if it doesn't scan properly (shouldn't be a problem with Tom's design), or if there is something else in the same bag that gets their attention (like drinking water, a nail file, or explosives).
One snag that people are going to run into is using approved bags in un-approved ways. An approved sleeve might have a small pocket (like the Brain Cell), and if the traveler keeps a power supply or something else in that pocket, it's going to fail the scan. Thankfully, Tom's design for the Checkpoint Flyer seems to avoid that possibility altogether, as all the pockets are on the other parts of the bag.