There's so many reasons that you never draft for need, and you certainly don't let a prospect in your system block you from drafting a position you feel a guy is BPA at.
First of all, these guys take 4-6 years to effectively reach the majors, even top college picks often take 2 years to develop into everyday players.
Players bust, get injured, and never pan out, and then a position you thought you were strong at becomes a weakness.
The point of a system is to supplement the big league club, and sometimes that is through trades. If you have a surplus of one thing, you can trade it for what you need.
If you had the #1 prospect in baseball, and he was a catcher, and you had a crystal ball that told you Davis would become the #2 prospect in baseball you draft him, you draft him all day. If both guys pan out you package one up for a TOTRS.