You never use any wax to fill or smooth seams on heated carom tables. Bondo or epoxy fillers only. You can apply the bondo when the slate is cold and you should have no issues with the seams after the slate heats up.
Keep in mind, the heat is designed to be run at 10-15 degrees above the ambient temperature of the room. IE. if the room temp is 70 degrees average, the heat should be set to 80-85 degrees.
The, heating elements that produce the heat under the slates can produce local area temperatures of 120 degrees plus. That is more than enough heat to soften or melt most of the billiard waxes on the market. The slate acts as a heat sink and will even out in temperature over time. The heating elements themselves, vary in wattage, spacing, efficiency and BTU ratings. Play it safe, use Bondo.
Jay