I think just by looking at how the two cups design is built the answer would be. 1. cost, you have more fittings to buy with this build. 2. it will be more work to build.
I think the Dual slate plate design is much cheaper to build and for me I though it was much simpler. It has been proven to work excellent ,There is now way it can produce higher abv. I honestly think once someone has made there condenser, with a slant plate design most novice builders could knock this out in a half a day easy. I dont see any way a column could be easier to build than a dual plate Bok. Its one length of pipe with two plates soldered in place... then 2 holes for themo, and take off port. Thats it!!
Once again just my thoughts i am sure many are different. Oh ya I posted the design just so everyone wont have to go and look it up.