"The reason is because the 1099K shows the credit card charges that the customer pays."

Let's restate this.

The Seller has to collect the full amount. Their processor will hold back fees, commissions, etc, and forward the Net.

You are confusing Banking and Sales.

Your client "got" the full amount. Then, their processor, when that applies, took care of their next step in sorting out the destination of various parts of the total paid. Your client does the same thing internally, if there is (as an example) a cash sale.

"deposit into the bank is much less because of the fees withheld"

The business financial records should show these fees as Expense. How do you manage a business and shop around for a better processing agent, if you don't track what you pay in fees already? How does the IRS know you have any business expenses if all you report is Net income?

You do not report only the outcome. You track and report everything. Just because it isn't in their hands when that step was done, doesn't mean they did not incur it. It was processed on their behalf and those are their fees.