For more regulated classes of drug the FDA doesn't just control the conditions under which it is made but also assigns production quotas to different manufacturers. The prime worry, I believe, is that if too much of a controlled substance is produced and it isn't sold then it might end up being sold illegally. There are also issues where allowing people to produce a drug willy-nilly would stretch the FDA's inspection capacity and allow the possibility of defective drugs being made.

Plus there's the issue of whether a drug can remain safe to use after long periods of time at all.