In my CAD programme (not solidworks) the blind hole is used to set the depth of the pilot hole, then the thread depth is usually set less than that so I don't need to tap right to the bottom. Basically the hole is over drilled in depth e.g hole is 15mm, thread to 10mm.

Also I have to do the counterbore and clearance hole in the top plate as a separate CAD operation to the threaded hole in the other plate. Are you trying to do all holes in one go in CAD? Not sure how solidworks offers this in the hole wizard but it could only apply to each part in turn, so 2 separate operations ?