It seems to me like I don't actually understand the exact problem you want to solve.
For me the main problem with navy factory pathing are the ~5 seconds after a unit is built being very inconsistent. It takes seemingly random paths, sometimes driving into a wall or the naval factory it was built from, and then just stopping there.
The problem could be summarized as: "Make navy unit roll of consistent for all queued movement directions"
This could, I think, be solved by having the ships phase through the factory that built them and adding two horizontal roll off points in addition to the two vertical roll of points that already exist.
Is your problem description closer to: "Make it impossible to block navy traffic with naval factories." ?