The laticrete waterproof sealer says to put a bead of silicone around the drain- before you lay the tile. This seems like it would be counterproductive since any water that has made it passed the grouted tile would have no where to drain. Without the silicone the sloped bed would naturally take any water to the drain where it would be able to find the weep holes. Should I ignore laticretes instruction and leave the drain silicone free?

Silicone wouldn't stop water from making its way to the weep holes, but regardless ... I've never used silicone around the drain.

Which Laticrete product are you using?