I have done extensive testing of both magic mortar and of flame holder. I've deduced that either the representation of the information we were given, and how they would stack together, is either wrong or misleading.
Flame Holder seems to work perfectly fine with every other Weaponskill I have tested, producing great results for Bone Crusher and String Shredder in particular. However, Flame Holder doesn't seem to work that same way with Magic Mortar.
A very good example is this test, which is just one of the many I performed.
Build the Automaton up to 3k TP, change gear to erase master TP to stop Inhibitor from inhibiting. Automaton HP is 1588/4264, melee skill is 408. Put up three maneuvers with Flame Holder equipped. Deploy Automaton against Blanched Mandragora in Ceizak Battlegrounds. Magic Mortar is performed immediately, does 5425 damage. Automaton kills Blanched Mandragora with melee strikes. Immediately afterwards, equip Empath Necklace in the neck slot to regen hp back to 1588/4264, remove as soon as it hits that. Put up three fire maneuvers, deploy against target from 17 yalms. Heat Capacitor 1&2 activate, giving Automaton 3k TP, erasing all fire maneuvers in the process. Magic Mortar goes off almost immediately afterwards, dealing 4744 damage. There was no time for the Automaton to get hit, or take any damage. The only difference between those two Magic Mortars are the three fire maneuvers.
Magic Mortar has a base modifier of 1.5 at 3k tp for damage gained from HP lost. So essentially "[Max HP-Current HP]1.5+Melee skill" should be the damage formula when the Automaton has 3k TP. If Flame Holder STACKS with the base damage of Magic Mortar, the formula would be "[Max HP-Current HP]4+Melee skill" at 3k tp. This clearly isn't the case from what I am observing. Camate specifically said that it works with the damage calculated from the Automaton's missing HP, but anywhere you throw a modifier as large as 2.5, you aren't going to see a result as small as an additional 681 damage.
How does Flame Holder work with Magic Mortar? Because these results indicate that it does not do what it does with every other Automaton Weaponskill I have tested.