If You Were Building a Deck......

Cantilevering a deck is perfectly acceptable practice - in fact, it's probably even preferred because you are hiding posts underneath the deck.

Placement of those posts doesn't have to be precise so long as the rules of 2 feet support for every one foot of cantilever are followed. Your beam doesn't need 3 posts so I'm confused by that.

It sounds to me like he's slightly lazy because he'll have all his equipment out to dig a 3rd piling so how much more effort would be required to dig the TWO required pilings with precise placement? That part confuses me based on your description but it's kinda hard to critique a man's work without the following:
1. Seeing the site or at least a drawing.
2. Hearing the rationale of the other contractor.

I don't like to second guess another contractor unless his work is very clearly shoddy and he's giving the rest of the us a bad name. He may have perfectly legitimate reasons that are not being adequately conveyed to you.

But if he's doing it wrong you should NOT be required to pay him to take it out and do it correctly. He should do that at his cost. However, if his support is adequate according to code and you're asking him to redo it simply because you don't like it then you should have to pay him.

It's hard to say without seeing the site.