as far as I'm aware, cubemap projection textures are just numbers. the entire image is loaded from disk with no consideration for actual entities nearby.
if you're getting z-fighting with shadows, there's a few things that can cause it.
if mixing glsl+fixed function, make sure your glsl code uses ftransform(), or the coords will not match exactly.
make sure any depthrange etc values are specified exactly the same.
GL_DEPTH_CLAMP_ARB, if used, needs to be set up the same way too, annoyingly enough, even when not clamping that pixel.
if you're recalculating things often, make sure you use exactly the same algorithm to interpolate etc each model, those coords must be exactly the same.
you should not need glPolygonOffset for anything other than attempting to fix z-fighting with coplaner world/submodel surfaces. If you do use it, make sure you use the same values for both your depth/ambient/fullbright passes and your rtlighting.
If you never enable it, your stencil shadows should function perfectly. Except for those coplaner surfaces.
I would expect this is the cause of your buggy lighting on plats, and possibly even models too.
if your lights etc are coplaner with any of the surfaces that they light, you may end up getting really fruity zfighting due to precision. For one pixel its infront, for the next its behind.