It makes all kind of sense to me. Shanahan is fascinated by running QBs. He was the OC in Washington when they drafted Robert Griffin and in his rookie year, he rushed 120 times for 815 yards. I think that Shanahan wanted to replicate that with Trey Lance, and that's why they drafted him. In his first game last year against the Bears, Shanahan had Lance rush 15 times for 54 yards. Even though it's not a sustainable strategy, you can see Shanahan loves that idea.
I think that if the 49ers had a first round pick, the deal would have been done already. Or maybe they would be trying to draft Anthony Richardson.