Magitek Command

The problem is not the Magitek command itself. Unless I'm mistaken, it's the animations of the spells tied to magitek command that does the animation intro and beam position. If you assign Fire 2 to the Magitek spell selection, I don't think your character will take the step forward.

This is correct. they are tied to the action animations, not the Magitek Command. If you put a magitek spell in your magic list, or activate it any other way (like a weapon proc or something) it will step forward, etc...