Yep, this is my take, the level of competition at NDSU inflated Trey's rushing capabilities and Kyle might have bought a lemon. When it comes to rushing lanes, the QB draws are supposed to make the rushing decisions simpler, he wasn't even being asked to do complex RPOs yet. If he can't do QB draws then he can't really do any rushing.
The way Shanahan is using Trey rushing is pretty much identical to the way Buffalo used Josh Allen rushing in his rookie year. I think Trey is only averaging like 2 more rushes a game at the same point in his career as Josh, which makes sense given how much more rushing Trey did in college than Josh. Buffalo actually increased Josh's rushing totals during the back half of his rookie career, so if we follow that plan then Kyle should be rushing Trey more next year. Using a mobile QB's legs is designed to slow the game down for the QB and let them get comfortable in the offense. People seem to want Kyle to use the Brock playbook and get rid of the designed runs, which is going to be a tougher system for a QB who had 1/3 of his production come from rushing in college.