This thread has a lot of interest for me.
First I need to say that I have not tried polyester type epoxy, therefore I do not have any hands on experience applying over the regular 50/50 mix type.
However...
My understanding of epoxies is that they essentially perform a mechanical bond to whatever it is applied to. To me, that means that it doesn't matter what is applied to but in order that it bond well there must be a rough surface or it will peel off. A simple light sanding usually suffices, as one might sand between coats of paint. Smooth surfaces present a huge problem with adhesion.
The fact that one mixes the epoxy with a hardener implies that the "cure" is chemically attained as opposed to drying out the solvents like most of the other glues we use. This cure should occur whether in the presence of air or not.
Since the first coat of one epoxy should be cured before an application of another type, chemical hindrance between the two types should not be an issue. Or is it in these cases?
Is the polyester chemically reacting in a negative manner to the 50/50?
If so, could this be thwarted by using some other substance between the two, such as a thin coat of polyurethane? Yeah, I realize this is not a good answer for several reasons but it is merely a suggestion.
Robert