Trek is pretty consistent, but they kept changing the spec on early frames as they added size and changed the tires (maybe wheels too).
To review - whatever the tire opening is -6mm on the smallest frame size or some toe overlap measurement, with the as-delivered wheels. The width of the rear tire opening is dictated by the seat stay opening, which is impacted by the length, BB height, BB Shell width, and the designed gearing (as the chainring cuts into the spaced needed for the tire).
AL and ALRs have completely different backends with regard to build. All the sizes have the same chainstay length, with the BB moved around to clear the tire.
AL Rear (38mm now quoted for all sizes): 5mm longer than the ALR; no adjustable dropouts; less fancy cable routing; narrower external BB housing
ALR Rear (45mm or 40mm 49 & 52cm due to toe overlap): fancier seat stay forming; 16mm(?) wider BB housing (internal) ; adjustable dropout;
So the ALR comes in less sizes, the seat stays have more bends, and the seat stays start further apart - there's a lot more room to put a tire in there.
The AL should really just be called the Domane, but they probably thought Checkpoint would sell better as you could tell an offroad story as you sold it. If you're going off road onto some thing with a deformable or ungroomed surface, you're much better served with the ALR frame. 38c is pretty decent, but 42c will let you lower tire pressures more over bumpy stuff and float over sand/rocks (which equals speed). The cable routing on the AL frame isn't open and not as desirable in muddy/ sandy conditions as there are more openings (I think you can run housing bow to stern on the ALR).