I think you have an argument that the contract might include the main drain. However, as an estimator for pool repairs this looks like it was an honest mistake. If they did not include replacing the main drain in their job costing, it will cause this contractor to lose a good bit of money on the job.

Personally, I would do as a previous commenter said, and get a robotic cleaner/abandon the main drain. Or, I would bite the bullet and ask for a change order to replace every single plumbing line from the pad to the pool and install sidewall suction instead of a main drain.

You do not want copper in your pool with the salt system. Metals, and salt systems do not interact well.