"The payroll withholding is pre-tax"

The entire $15k is in box 14. Ooof. You can't eliminate that $6k as gross pay and also ignore that $6k for health coverage box 14, though. It's now the opposite of a double-dip. See if this helps:

Basically, then, they're including this as compensation with the appropriate tax treatment as health as if it is paid to the provider, but mistreated for income tax, and then holding it back? Because this $6k isn't supposed to be paid out to the employee; it's part of what is sent to the health coverage provider. That doesn't affect its reportability. So yes, it is part of taxable income and part of what is reported in Box 14.

Pre-tax deduction is not fully the correct status. It is not subject to Social Security, Medicare or FUTA. Paid to the health coverage provider = Box 14 reporting. Isn't subject to income tax withholding, but is reportable taxable income. That's because the shareholder will most likely take it as deduction on the 1040. Otherwise, there should be income tax withholding on it. That's why pre-tax payroll deduction isn't exactly the right treatment.

"only add to the W-2 compensation the amount of $9K to the W-2 for SCorp Medical as the $6K was already pretax and reduced the employees Box 1 wages."

That's the usual employee benefit treatment, which this shareholder doesn't qualify for. The company isn't being reimbursed for the $6k. They are sidestepping the fact that it is sent in as a health coverage payment, along with their $9k. This person's W2 should show $15k as gross compensation, and that amount is not subject to Social Security, Medicare or FUTA. It is part of Taxable income, as part of gross. They are just handling the two portions separately, but the same way.

What they did, then, these are equivalent and just semantics:

Your salary is $52k and we provide $15k health coverage benefit on your behalf which is reported as taxable income to you. The $15k is in box 14.

Or,

Your reportable taxable salary is $67, but $15k is not taxed for Social Security, Medicare or FUTA, and we send that for your health coverage. This $15k is in box 14.

Or,

Your salary is $61k; we keep back $6k untaxed for your health coverage and match that with $9k on your behalf. The $15k total is reported as taxable income to you and is in box 14.

The difference would come from when a person has a stated salary and does not participate in the health coverage. That's why their method is odd.

The company is supposed to pay to the health coverage provider or to reimburse the employee for qualifying coverage paid by the employee. They're sort of doing it half-and-half. Where they have it wrong is that the employee-paid share is not supposed to be first paid to the employee with the tax benefit intact.