If you don't have a Pro Bowler at a position, or you have reason to believe you might lose the one you have in 3 years, and you have the chance to draft a Pro Bowler, then you draft the Pro Bowler. Reaching for needs is how you get awful drafts like what the Chiefs and Cowboys trot out year after year. RB is the highest attrition position in the game. Getting a long-term workhorse like Gore or Steven Jackson or Adrian Peterson is rare. So if you want a stable run game, you have to plan as if your current starter won't be productive 3 years down the road. The luxury of the Shanahan offense is that you can invest 4th, 5th, 6th and 7th rounders and get a quality player at RB. But you have to maintain that pipeline.
You simply cannot go into the draft with the mindset of "we need a safety and our RB just ran for 1500 yards, so let's take the safety we graded as a 3rd rounder over the RB we rated as a first rounder". Until the differences between the BPA at need position and the overall BPA are the equivalent of 5-10 draft spots, you go with the BPA.