The issue was never that the magistrate judge would be setting the precedent. No matter who prevailed, there is going to be an appeal and that's when precedent would be set. Even at that point, a negative ruling wouldn't necessarily be an insurmountable problem for the FBI as it wouldn't be binding until the issue has been decided by higher authority. It could still be cited as an example of persuasive authority (i.e. something other courts
may follow) before then, but that's not the same as being
binding.
So the FBI would have a lot of time before they had to worry about the consequences of a negative ruling, and they could drop the matter well before any precedent was set. Apple is in a trickier situation, in that once they've done the work, it becomes more likely that they'll face additional demands in other courts, or--and this is the worst case scenario--a few boneheaded legislators try to pass legislation on this issue. They've got a lot less room to work in, so if they could make this go away in front of a district magistrate without ever having to worry about setting any precedent (even if in their favor), they probably would.
0. http://www.law.georgetown.edu/academics/academic-programs/le...
1. http://faculty.law.lsu.edu/toddbruno/mandatory_v__persuasive...