So you are the seller.
You recieved an offer from a US customer
You counteroffered, but noticed that your copy of the counteroffer gives the domestic shipping cost.
When you changed the shipping option to USA, the amount of shipping changed.
You are right that shipping is never part of the offer/counteroffer process.
You are forgetting that your US customer sees the shipping to his address provided you originally had a shipping fee to the USA.
You also are forgetting that sellers are not required to accept payment for domestic shipping costs if the customer is outside Canada.
So what you originally saw, is not what your customer is seeing. The programming is unable to "see" where your customer is located, I imagine.
That's my take on it anyway.
And this is one more reason why I don't think Best Offers are a good way to make sales.