FWIW, even when these were new, the wagons seemed to be most commonly equipped ALH+manual. The rare ones were the gassers, and the rarest one (as I have only ever even seen ONE) is a VR6 wagon. And that ONE I saw, I actually walked past in a parking lot and noticed the VR6 tag on its hatch.... I stopped and walked around it and noted it had 16" wheels, big front brakes, so I took a pic of the VIN tag and checked when I got back to the shop.... yep, natural born VR6 automatic GLS wagon w/ lux. Never saw another.
I think the common sense and utility a wagon offers couples with the same part of the brain that would want the diesel and the manual gearbox. The diesel wagons were SO popular, that right up until Dieselgate's fecal fan event, Volkswagen was considering making the TDI the sole engine option for the G/J wagons here, as the gassers were just not selling. I've only seen a few gasser A5 wagons, too.
I also had a customer once with a 2000 Jetta sedan, GLS, withOUT lux (so, steelies and no sunroof), with a VR6 and automatic. Only one of those I've ever seen, too. Most VR6 sedans were fully tarted GLS or GLX.