IIRC, Q3Map2 does support vertex RGBA colours on model materials, but the ASE model format only supports RGB. This is why Q3Map2_fs was hacked to (somewhat incorrectly) use the RGB values on ASE models as the vertex alpha value. I believe if using other model formats like OBJ you can skip the use of Q3Map2_fs completely, but I've found getting OBJ materials out of 3ds Max and into Q3 difficult so I never investigated this further.
Otherwise, sock has some great terrain tutorials that are defintely worth the read: