The wheels have been changed a couple of times over the years. Early issues used compact car tires (the ones used in Corvair and Opel GT kits for stock). Most of the early variations (Covered Wagon, Topless Pick-Up) had the same parts in different boxes, with instructions for cutting the top. I've heard those versions were done because the Deora was a slow seller. The slant six engine is cool now, but kids buying kits back then probably weren't too crazy about it. At the very least, AMT should have made the engine cover a separate piece molded in clear, so you could see the engine from up top.
The Alexander's Drag Time was a DIY project in a box. The engine was the Hot Rod Shop (AMT parts pack) 392 Hemi, unplated. The whole tree was tossed in, so you got the Corvair engine along with it. The builder was supposed to radius the rear wheel openings, trim out the molded-in engine cover, and cut off the top. Trim lines may have been added to the inside of the body for the wheel openings, but you were on your own for the rest (and that plastic was pretty thick). I don't know what was included for tires, but if I remember right you were supposed to use the slant six engine's U-shaped display stand to make a roll bar.
I've got an early Seventies issue with larger wheels and tires. The two sets of compact car wheels were replaced by the reversed/baby Moon set that is still in the kit, and a set of "Flag" mags that appeared in a few other AMT kits in the late Sixties. These were later changed out and replaced with the four-slot wheels that are still in the kit. This issue still has the clear canopy, and has a couple of surfboards that AMT put into a few other kits around that time The flat tonneau cover for the bed area is still included also. The next issue after that was the mid-Seventies "Vantasy" with the camper shell. I don't think the clear canopy reappeared from that point on.
You're correct mark, the clear canopy and the tonneau cover went to A M T's unknown area aka Area 69!