I suggest just paying it.
I really don't see the electrician coming down on his price, and I don't see the contractor making a concession out of his contract. He never made an allowance for it on his spread. The price the electrician is asking is the fair market value of the upgrade to 100 amps regardless of how much the additional materials cost.
If he proceeds with his multiple breakers installation it's going to take 5 slots in your existing breaker box. It'll be 2 double throw 30's and a single throw 15 for the pool lamps.
Another option would be to ask the builder if you purchased the materials would the electrician install it on your behalf, all he'd be out is the same labor it would of taken to begin with.

See ya,
Kelly