They don't really leave it out of the equation, though they don't explicitly state how it factors in. The issue is that a high profile case that people want to be prosecuted to the fullest extent is being used as a wedge to force a large undertaking (producing the unsecure firmware) to be made. Future requests from law enforcement on much smaller cases would then only require the smaller undertaking (signing the existing firmware), and resisting that court order would be significantly more difficult.
If the court decides that they're obligated to comply, then that should apply in all similar cases. Resisting that order would be more difficult because they already lost the battle, not because they already created the tool.
My point is that it would also apply in a smaller cases for a different reason than simple precedent: it would require no significant work not already undertaken.
But why would that be bad? It shouldn't require significant additional work, even in smaller cases. If the FBI is getting warrants to access things without actual probable cause, then we need to be outraged about that issue, not how they get access.
