epoxy will bond well to polyester - polyester won't bond well to epoxy... that's the first rule you need to keep in mind while working with composites. 
BUT when you've properly released your mould with release agent you shouldn't have any problem. Would recommend you a chemical release agent to be sure. 

I make all my moulds with the Uni-mould systems and do 90% of epoxy parts in them without any problems.

Epoxy should in theory be stronger, stiffer for moulds than polyester.
Polyester would be subjected to more shrink/warping and less high temp resistant BUT the uni-mould system is a very stable polyester based system that can be polished to high gloss and a thick CSM + toolingresin build-up can be done in 1 go