Epoxy and Polyester have different thermal expansion (and cure) rates.
Better to fill the holes with epoxy in the bottom for adhesion (if
needed), and then fill the 'upper' part of the holes with polyester.

Most of the gelcoat repair 'artists' I know NEVER use epoxy for blemish
repair for the above reason. If you keep the repair materials
composition as close to the original base materials, usually the more
mechanically stable outcome will be the result.