Although wasteful, I have found for me the best way to get the clean seam line (assuming it's a straight parting line and not wavy or contoured) is to apply the clay bed but no all the way up to the part line, model the clay just bellow it... Now the sneaky secret I use, get some silicone thinner, and mix up a very small batch of silicone with say 10%-20% thinner added, this will make it pour, degas and self level much more readily... You are not really worried about the integrity of the thinned down silicone you are basically just using Mother Nature to create a level surface bed
Anyway with the mold on a level surface (I keep some shims handy just in case it needs some adjustment) pour this super thinned out silicone into the mold, just a skim coating of it over the existing clay bed bringing you up to the part line... Let it cure until firm, you don't really have to wait until it's fully cured, spray on some release and then pour that side... When you flip it over and pull out the clay, simply remove the thin sheet of silicone from that initial pour and you have a SMOOTH finish and clean parting line...
And if you are like me that HATES cleaning clay off the master and doesn't care about wasting a little more silicone you can just clay up close to the part and use the same technique of letting the initial skim coat silicone fill in the void...
For me personally the few dollars or so of wasted silicone is well worth the cost in labor savings and frustration...