I don't analyze network type, when creating marked trails. There is no difference between 2 lcn and rcn + lcn. But are you sure that 2 overlapping lcn would be visible on map if they share the same pattern and maybe the same length of reference number?
I see other problem, I remove trails, which have no defined colour, if there is other trail on the same way. Maybe not a good simplification, but my goal was to get colour trails.
Could you point an example on map?