I've worked with 3D prints I've made and with some of the "experiments" I've done with baking clay and adding to the designs with RC-3, I'd be a little hesitant to use anything that heats up a lot during curing. Vac 50 is listed as a "resin" so I would always assume all resins heat up as I know RC-3, the Flex series, and the Clears all heat up. Though the Clears heat up in a slower fashion, they DO still heat up.
That being said, I have not used the Vac 50 so I'm not sure exactly how hot it gets when it's curing so it may or may not melt your print. When I need to add to a print with the RC-3, I'm basically using "drips" which don't get that hot due to their smaller size but you want to make a mold with the Vac 50 which implies it will be of a larger size and therefore might be large enough to generate enough heat to melt or at least deform a print - I print ABS at 240 degrees so (to me) anything that goes over 200 degrees would cause the print to deform and I would not attempt using it.
So the question is this : is this a print that needs to keep its shape and how worried are you about it whether or not it might get ruined? Personally, I would make a silicone mold of the print, cast a resin copy of it and use the copy to make the Vac 50 mold. That way if the resin copy gets ruined you will still have your original 3D print in perfect shape.
My print is in PLA so I might have to use your approach. It's going to be a two-piece mold. I used Plat 55 but after maybe a 50 runs it starts to deteriorate on me. By the way, I'm pouring/injecting plastisol into the molds. I see they discontinued Plat 55 and replaced it with PlatSil 73-60. I wonder if that is better?
I can make a silicone mold of it but the part that I'm not confident in is making the vac50 mold from that cast. Right now my process is to 3d print two halves. I affix one half to glass, build a box around it and pour. Once cured I glue together the halves and pour the remanded half of the mold. When I do it this way my seam line is barely visible. I don't know any other way to do it really.
Ah yes, if it's PLA then definitely make the copy. The PlatSil 73-60 is probably better, when they reformulated Plat 25 to take out the yellow dye I noticed the Plat 25 works a little better than the old formula.
Sounds like you've got the right process down. Doing the Vac 50 should the same process. Now if you're joining two halves of the same product, you can use the same product as a glue similar to pouring "layers" in resin pours.