When I first started considering buying an R9T last summer, I focused at first on the Scrambler because I loved the looks of the bike. As I learned more about the lineup, I switched to seeking a Pure due its tighter fork angle and shorter wheelbase, shorter seat height (I have short legs for my height), and because more Pures came with the cast/mag wheels than spoke wheels (I didn't want spokes). I just wanted the more agile bike, plus I knew I would never be riding off-road.
So besides the wheel size difference, you are likely looking at steering difference, too. But I don't think these differences are monumental. I would think -- and this may be the voice of inexperience talking -- for gravel and dirt roads, tires would make the biggest difference, followed by suspension, depending on how good or bad those roads are. I also wonder whether a lowered Scrambler also has reduced suspension travel. I'm not positive, but I think on the big GS bikes they do have shorter travel.
As for the standard Scrambler, I just checked the 2021 specs, and here are the differences between it and the Pure:
Wheelbase -- Scrambler 60.1" vs. Pure 58.8"
Steering head angle -- Scrambler 60.1 degrees vs. Pure 63.4 degrees
Suspension travel - front/rear -- Scrambler 4.9"/5.5" vs. Pure 4.7"/4.7"
