I think the only way to deal with this is to buy the correct postage yourself and cancel the ebsy label.
If your buyer has not paid enough I am afraid that you cannot ask for more.
I also think it is up to you to be aware of postal requirements in terms of size and weights, and to identify when ebay give the wrong option and cost.
For example if you say it is a large box, it should be easy to see if ebay is charging for a large letter.