Also having a hard time making terrain. I remember making terrain in GTK radiant years ago, but now I forgot how I did it.
Open up baseq3/scripts/default_project.proj in a text editor. That is where the Bspc menu option is "compiled" from. It is an XML file which you can edit. Add, remove or change the compile features to suit you. Best to make a backup first.
You could make your own "project" or "game" with build options too. Check out the installs directory. Make a copy of the Q3Pack. It has been a long time since I modified GtkRadiant like this, so I can not remember which files are important (or need to be edited). I just use my customer build script instead now :]
Edited 3 days after the original posting.
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