To be honest, in my experience, it's quite acceptable to use epoxy fillers (like milliput) with polyester hulls, and polyester fillers with epoxy hulls. As they're both thermoset resins, any difference in expansion rates is so tiny as to be negligible.
For instance I find epoxy fillers are far more rugged than polyester fillers. So they're useful in areas prone to stress, or if I need to fill something that requires a sharp point. On the downside, epoxy fillers are an arm and a leg, and in Milliput form at least, are a bit stiff to work with, plus they're slow cure. For larger areas, and general filling duties, I switch to polyester filler.
Problems tend to occur when you mix very different materials together, like wood and plastic, plastic and metal or thermosplastics (polystyrene, ABS etc.) with thermoset plastics (epoxy, polyester, bakelite etc.).
Having said that, you can get away with a lot if you join them together with a flexible adhesive like silicone rubber or (better) Sikaflex.