It is important to understand that the dealer can certainly detect (if they choose to do so) changes to the ECU's ROM. This would occur when you install the AccessPORT (or any other solution that tunes the ECU via a reflash). When a dealership employee explains these types of methods to someone, they are most likely talking about this kind of detection.
The gray area is whether or not the dealer can detect changes to the ECU that have been made in the past AFTER the ECU's ROM has been put back to its original state before the aftermarket ROM was flashed. This would be the case if you properly uninstalled the AccessPORT v2 (or with other solutions, reflashed the original stock ROM assuming you backed it up). To date, we have not seen any credible evidence of this. Doesn't mean that it doesn't exist or that it will not be added in the future, however. Some other manufacturers do have this capability, so it is not impossible.
The dealer could determine that an ECU reset has occurred recently by looking at specific OBD/SSM parameters. An ECU reset will occur when the ROM is reflashed. However, the same thing will occur when you disconnect the car's battery, so, it is certainly not a foolproof means of determining anything for certain (of course, that may not matter depending on the dealer or if there's evidence of other current or prior modifications).