I use Reynolds Advanced Materials (Smooth-On) Products. For most molds I use Mold-Max 25. For casting resin I use Smooth-Cast 300. While both have spec'd shrinkage I have found it to be far less if used properly. Which means don't over-catalyze and don't heat cure. Thick parts will tend of shrink a bit more than thin ones due to exo-therm (heating up while curing. Another trick is to let the silicone mold sit for a week before demolding from the pattern. Yes, the instructions for the material say it can be demolded in 24 hours, and I do for some non-critical parts, the mold will last longer and seem to have less shrinkage if left to cure for a week before using.
As far as clearances, those can vary from .003" to .0075" depending on the part and function. For pivot holes, like the one in the thumb wheel I print the part slightly undersize and ream out on a drill press to the proper end size.