I'm quite sure that this method works perfectly.
I detail what I did:
In Slovenia map (your post above) we have 3 bad rail intersections. Locations are:
- Ljubljana
- Zagreb
- Karlovac
With the actual database (only 2 WP in these 3 locations), it's quite impossible to cross these locations with good results: false virtual WP, some trains stop everywhere, some trains go forward then reward...
Then I added 1 third WP: result was better but not correct in the 3 locations
Then I added 2 more WP (5 WP): Trains crossed these locations without errors.
You can see these screenshots with my orders when mission was analyzed (time of mission/flight = 2H00). Trains are exactly where they were ordered except collisions
Ljubljana
Zagreb & Karlovac
"I just need to know that in every other respect the rail routes are correct (no overlapping routes "
If we add 3 WP to all 2WP-segment, then bad intersections will be only real bad intersections (overlapping routes). I guess that the number will decrease a lot, specially for trains.