If you make a section of the bitmap transparent, it's transparent, period.
And, since it's transparent, and shapes that can't be seen are not textured (since there's no need to normally) you'd just see right through to the terrain.
So the solution is segregate the "underneath" section of the dash from the "custom" portion.
The skin dictates the "underneath" texture and guarantees that it will be opaque so that even if the "custom" dash is completely transparent, it's only see-through down to the skin-dash.
This way, we wouldn't have to modify the skins - if you want the old (i.e., ones defined by the skin) indicators just set full transparency on the custom dash.
It's redundant, sure, but it solves both problems - wanting a custom dash and preventing the use of a transparent dash to cheat.