Re: "...the company has agreed..."
Paying taxes is always a negotiation because you prepare your own taxes. You pay what the forms you or your CPA prepared say you owe, and the tax authority may or may not question your preparation. If they do, you can defend all/part/none of your calculations, implicitly accepting theirs where you choose not to defend.
If they disagree with your defense of your preparation then you have to prove it to them (at least in the US - since the IRS are considered experts if you can't prove to them you're right, then by default they're right) and in the end you mutually on an amount and settle up.
If you ever receive a big bill that you owe more in taxes, and just pay it without question (unless you knew you were trying to get away with something and they caught you) then you're stupid. It is worth fighting if you and your CPA believe you're in the right, I know this from personal experience.