Think the problem is that for procedural junctions to work the track has to be physically joined, with a crossover there is no physical connection between the tracks other than one is placed over the other.
Would I guess need a different method to achieve realism.
Surely not beyond the ability of N3V's intrepid coder(s) though. The track laying system in DTG TS works along similar lines and can form diamond crossings which are integrated into the train protection database. MSTS of course used fixed track pieces to place diamonds, possibly a way forward for Trainz but they need to adapt to the spline type being connected and the code still needs to recognise and protect against conflicting movements.