The technique for this is:
1) determine "border cases": cases where the shortest path is the same (as far as the number of systems visited) but the systems traversed is different, and cases where the path is shorter is you permit jump-holes.
2) look for patterns in the preference (as indicated by the vanilla fl path.ini files). Does it always prefer jump-gates, all other things being equal? Does it prefer jump-holes only if they lead to a shorter route? Etc.
Another thing you can check: if the game has a one-off flag for the Li01-Iw03 jump-gate. You can check this by putting this as a viable path in system_shortest_path.ini, then loading up a savegame post-mission-4 pre-mission-5, and gain a level in the NY system. If you get routed through the Li01-Iw03 jump gate, you know that the only difference is the path.ini file. If you do not, you know the game is making a weird one-off exception.