First off I will start by saying I own both and agree that the BC125AT has a slight advantage over the BCD396XT and it's by no surprise either...
The BC125AT is not as wideband as the BCD396XT; it doesn't cover ANYTHING higher than 512MHz. That allows the receiver to be better filtered and isolated from outside images, mixing, etc.
The more wideband coverage a receiver has, the worse things will generally get as there is a delicate balance between cost of engineering vs performance. Can a wideband receiver be made with good performance, sure, but it's going to cost allot more than a $500 scanner.
What I use my BC125AT for is scanning amateur radio repeater and simplex frequencies for activity. Also for AM aircraft, GMRS, FRS, and other services that are VHF/UHF; it's the best radio for it and for under $100, you can't beat this radio for VHF/UHF work on the cheap.
On a more future note, I am in the process of comparing both of these scanners alongside my new BCD436HP to see how the performance is; however, I expect the same or similar results given it another wideband receiver...