I had another thought about this issue this morning. Could anyone with some calipers measure the length of stem's cross on the x and y axis and compare that to Cherry or Gat stems? If not I might be able to borrow some calipers from a friend and check it myself, but Im wondering if the stem is slightly longer in those areas in addition to being a smidge wider.
Too lazy to take pictures but here were my measurements
using this caliper (included a Cherry Clear since those are a notoriously tight fit):
Box Royal X-Axis Length: 3.96mm
Cherry Red X-Axis Length: 3.98mm
Cherry Clear X-Axis Length: 3.97mm
Box Royal Y-Axis Length: 3.93mm
Cherry Red Y-Axis Length: 3.98mm
Cherry Clear Y-Axis Length: 3.94mm
So while this wasn't super scientific since I only did one switch each (took the measurements a few times), it's probably still fair to say that it's just the X-axis width of the Box switches causing the issue.
I actually tried doing width measurements for each of them but found that my numbers differed depending specifically where and at what angle I was measuring along the stem. I ultimately settled on just holding the caliper completely vertical and flush against the opposing axis, running the full length of the stem (had to break off the box of the Royal). So take the actual numbers with a grain of salt, but I think for comparison purposes they're somewhat useful at least:
Box Royal X-Axis Width: 1.32mm
Cherry Red X-Axis Width: 1.25mm
Cherry Clear X-Axis Width: 1.25mm
Box Royal Y-Axis Width: 1.10mm
Cherry Red Y-Axis Width: 1.09mm
Cherry Clear Y-Axis Width: 1.20mm
So again, while not very scientific it looks like the Box's X-axis width is the culprit. But interestingly it seems that the Clear's tight fit is due to the Y-axis width. So I wonder if that means keycaps are designed to have the same amount of space on both the X and Y axes, as then it'd make sense that the Clears are tight but not to a degree that they do damage (since their Y is still less than the X that the caps would be presumably designed to fit).
Edit: Decided to try my hand at measuring the inside of a Cherry cap and while it was incredibly difficult to get anything consistent due to the caliper not really fitting (anywhere between 1.21-1.26mm), looks like both axes are pretty close to the same if not so. So that would explain Cherry Clears.