While I haven't specifically tried to bond silicone caulking to GI-1000, I do work with with GI-1000 all the time. My advice would be to order more GI-1000 catalyst and finish the mold properly, although they may bond, im doubtful it would be a strong bond and could lead it to delaminate from the GI-1000 later, as well as taking days to fully cure. Silicone caulking also tends to shrink a lot after curing which could distort future castings and is not the same durometer as GI-1000.
The money you spend to finish the mold the proper way, will most likely save you time, money and the headache/heartache of poor quality casts coming out later.