I've done next to nothing in Edge job setups using Flexi. In Omega, pretty much the same thing will happen because the Edge turns up the heat for an overprint thus requiring a separate pass. Gerber's solution was to provide a third setting called "Overlap". This setting causes the foil to overprint the underlying layer but without turning up the heat. You may want to check for a similar setting in Flexi. If it isn't there, then getting Omega may be your only solution.