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Excellent, so it turned out the actual policies are not all crazy!
Thanks for posting, hopefully the next person it happens to will contact ebay and resolve this before paying.

This is an excellent question to ask ebay as they know exactly what boxes they provide for the sellers. I also think it would have been even better if you had done it when this happened, not many...

Adding non-disclosed fees AFTER the end of the auction is problematic. I don't think this is legitimate and would dispute it.
Other than that, if you bid based on your total cost, which I think is...