Why would the overlay need to be with the board that had a coating? Buy two boards, cover the parts on one board that are silver, shoot IR. Use second board for visible wavelength photo, combine for a beautiful overlay result.
Wouldn't that change the heat dissipation characteristics and skew the results? Is a metal surface coated with epoxy exactly the same (from transmission, convection and radiation point of views) as a naked metal surface?
Ideally you'd want to coat any metal surface with black epoxy, and set the IR camera Emissivity Coefficient to 0.9 (the coefficient for black epoxy).