A lot of great insight. I would only add, what were the specifics of the original agreement? Was it a lump sum or did you have to provide unit prices? Were there qualifications or specs that indicated they could add or delete based on unit prices? I agree try and leave the first agreement alone. Pipe and fitting were cheaper back then. Pipe and fittings are going up now. That's reflected in your new proposal.
I see it the same way. If it was a bulk price for the job “up to 2,000 trees” then the price is the price for the job. On the other hand, if it was unit price with an allowance in the contract for up to 2,000, then the invoice should have been unit billed. Water under the bridge at this point.
I can think of a job I ran long ago where most of the job was by unit with allowances. The sub was lightening quick with change orders if something went over but it was a rough slog to get acknowledgement of a credit when it went under. Would never work with that company again. I guess the moral of the story is if the contract is bulk price so it’s looked at as it‘s all a wash in the long run, then that’s the deal. If it’s unit, then fairness would seem to require a count and a true up at the end.