Your problem in both cases, I believe, is that the Bacon Mod does something that the game's pathing algorithm is not designed to handle. Specifically, the Bacon Mod makes it significantly more likely that a ship will encounter a neutral wide-area jump inhibition field in the vicinity of its origin, its destination, or both centered on something far enough away from the origin or terminus of a ship's path that the way in which the ship crosses the field has a nontrivial impact on total travel time and thus fuel required to make the trip.
The game's pathing algorithm is to the best of my knowledge a simple minimum-distance algorithm, which is fine in the unmodded game because all jump inhibition fields are small and the vast majority are centered on things very close to or coincident with the origins or termini of most paths anyways. The "gravity wells" that the Bacon Mod adds to stars - system-scale jump inhibition fields centered on the star - will in many cases make the minimum distance-path a bad path, at least insofar as far as fuel economy and travel time are concerned, because the minimum-distance path will often have a ship crossing a significant part of a system-scale jump inhibition field at sublight cruise speed, and traveling at sublight cruise speed is significantly slower and consumes significantly more fuel per unit of distance traveled than traveling at hyperspeed. Essentially, the Bacon Mod's "gravity wells" break the game's pathing algorithm - not so badly that the game doesn't work, but badly enough that you're likely to be better off manually ordering ships to proceed to the nearest point on the system boundary and then to their actual destination than to order ships to go directly to their actual destination.