Its a very long time since I have done any scenery design for CFS2. And never with FSSC so I am not familiar with the options that might be available

Bleedthrough is a z-buffer problem. If you can get at the scasm code you could add a ZBias( 1 ) before the poly and ZBias( 0 ) after

Layers I seem to remember work best when you use multiples of 4 for the number. ie if your first poly is layer 0 then the overlying poly should be layer 4 or 8

As I say it is a long time since I have done any of this. Most of my recent work has been for FSX and using the Terrain tools to merge phototextures into the actual terrain so this sort of problem doesn`t arise