So in the book they have the NPC "Military Leader" and he has +Tactician and +Natural Leader. Now other than the obvious use for Social/Mental based rolls one would have to do, how would this be useful in a combat situation? Would his mere presence inspire his men and get +1 positive die during their combat?

I would say that the answer to that and to a lot of other questions like it is "Yes - so long as it makes sense in the story"

My main concern would be as far as they apply to the PCs. It would need to be a static boost as far as they are concerned unless I forced them to make a speech every time. Where as if they are an established leader, the 'lead PC" mere presence would inspire confidence therefore...

If an NPC leader is leading PCs, or NPCs really, he could direct/order where they should direct their attacks. "concentrate all fire and that super star destroyer" kinda thing. Attacks directed against the target would get bonus dice. I could see this useful if you decide to fight one of those Horrifying Abominations things in Under the Skin. Or even to counter Voodoo Shamans and such. He could point out enemy weaknesses, and if the PCs use those weaknesses they could get extra dice. The leader could make certain tests easier, like a +2, instead of the normal +1 for extra help.

There is alot you can do here,

I like the "Mark Target" idea.