Probably mode of energy transfer. Microwaves are extremely efficient with transferring energy to water since you do not need to have something with higher temperature to produce heat flow. Also, you can heat up a contained area (especially water vapor) easily where as heating elements are limited to surface area (and the heat flow will be extremely low since the mass is low).

Their Zeal thruster uses a heating element: http://momentus.space/services/

To answer your question, I would guess that a microwave can get the reaction mass hotter than just a resistive heating element, and thus get higher exhaust velocity.