Derek, I have run into this problem in modded games in reverse, which helps pinpoint the issue. Instead of using the character's normal scale, the scale of the mount is used but forcibly set to 1. Warg Mounts have a <Scale>2.6</Scale> but this gets reduced to 1, making the mount much smaller than intended. The rider goes along for the ride in scale reduction, possibly because the mount skeleton contains an LCF point that modifies the rider's size. Skeleton shrinks = mount shrinks = rider shrinks.
The issue I ran into in reverse while modding was that I used Slags and Drakes as mounts. These modded mount skeletons have a much larger size and therefore require a much smaller scale - <Scale>0.32</Scale>. That makes them roughly the size of normal mounts. However, in cloth mode (just like wargs) these mounts get their scale forcibly set to 1, becoming 3 times larger on the cloth map.