I think if Mahomes had another year under his belt, he'd probably be a first rounder anyway. I don't know if the value was there for what they did, but if he pans out into a franchise quarterback, they're not going to miss those third rounders.
The question for me is: why move up one spot? The 49ers weren't going to take him. The scenario rolling around in my head was that, the Bears weren't the only ones trying to land a hopeful franchise QB, someone called the Bears snooping for a trade up, this caused the Bears to panic worrying that someone might call San Fran offering to do the same, so Chicago bit the bullet and did it themselves.