Flexible Molding Material

First question is which silicone are you using and what latex?

Now as to using a 3D print to make a mold, I agree that having to melt it again to demold is a big pain and you shouldn't need to do that just to get it out. I've used a lot of prints in my mold designs and have never had to do that. I use ABS and have done lots of finishing on them using different things from sanding/grinding to acetone smoothing to simply sealing them with resin. After I've done work on getting the prints right, I would never intentionally remelt them to demold from a mold. Especially since you can simply make cuts in the silicone (where needed) to demold.

Alumilite has a flexible series of resins - www.alumilite.com/products/resins/rubbers/ that work well with demolding from silicones. Just remember that they ARE a resin type and read all the instructions on how to mix and use them. I wouldn't recommend pouring them over the 3D print but they would work just fine as the casting material.

As for the mold itself, I would use High Strength 3 (or 2) as the mold as both are very flexible and #3 is a little "softer" than #2 but both can be stretched to demold without breaking a print without getting out of shape. The High Strength series is flexible but very strong so if you need to make a cut be sure to use either scissors or a knife as they'll stretch way before they tear and it's not easy to tear them.