Deductions & credits

What about if the organization in this example decides to allow them to add an additional 40 to "cover the cost" of the transaction fee so that $2000 is still net to the organization.  So the transaction is $2040 to the donor, but the organization is still going to have a 2% fee in this example from the $2040 which would net $1999.20.  Shouldn't the donor still deduct the transaction as it shows on their statement the full $2040?  They choose to have it go towards the fees but in fact it's an additional donation to the organization.