Let's try this again:

"which is usually what the term owner means."

No; the Supreme Court has declared that a Corporation is its own Entity. There is no Owner.

"So the SEP account does belong to the shareholder-employee"

But not part of the Company Financial data, not tracked here, and is only a Cash Flow activity for the business. It's like paying Rent. There is no Account to Manage the activity or balances because this is not a Company Investment account. It is personal for the Employee.

"who has 100% ownership of the company. This year, he chose to do a 100% employer contribution to the SEP, which cannot be run through payroll on QuickBooks Online Payroll"

It's just Spending. It's money Out. There is no Bank. You post it as Expense. It's like paying Rent.

"I can certainly reverse the journal entry I used to establish the tracking account of type bank for the SEP"

This is the Error. There is no Bank and there is no Tracking the SEP. Let's try it like this:

You are their employee. They put in money on your behalf. They do not track your Retirement Account holding(s). It's the same thing you just described, that the Company would have a Bank account to track Your retirement holdings. That is the Error.

"which matches the liability for the SEP that still remains on the books indicating that the SEP does not belong to the business but to the employee."

Let's try this part:

I write a Check to pay out the Expense. If I accrued the Expense into liability, I later pay out the Liability. There is no Bank here. And Bank is Asset. All we have is either Expense; or Accrued Expense as Liability to be paid out later, the same ad Employer pays FUTA or Worker Comp or General Liability insurance.

"Technically there is no other liability, since it has been sent to the brokerage already by the 100% shareholder-employee."

Sent "by" the Employee is also an Error. The company sends the funds for Employer-only. And if this was Paid already, there is no Liability tracking. Again, it's like paying Rent: Enter the Spending. Done.

"The expense for retirement plan has already been recorded against the bank account."

The Spending is part of the bank account or credit card used to make the payment.

The Details are what just got paid for.

I enter on the Check from Checking, the expense for employee retirement.

You have deeply overthought this and are tracking the wrong things.