There is a bug/feature request regarding the clipper tool. Actually on cutting brushes results look different from expected. Level/content flags are not applied to new faces, shader is set to default (nodraw).
There are different ways how this could be improved:
level/contentflags
1) apply diff of content/surfaceflags of all brush faces to new one (e.g. all have levelflags set -> apply those)
2) apply some voting diff (e.g. most of the faces have one flag set -> apply those flags that have some majority)
texture
actually it seems that texture is set to nodraw. Here we also could set
a) diff texture (if all have the same, set it to new, otherwise nodraw)
b) voting diff: apply the texture that is used by most of the faces
I did not look into the code, but this could probably also be applied to subtract and other face-generating tools.
Any suggestions?