I'm not sure where you would be contemplating entering a self-employed SEP IRA contribution twice. A SEP IRA contribution is entered in the Other Business Situations section under Wages & Income. It is not to be entered anywhere under Deductions & Credits.
The reference you provided only has you entering a SEP IRA once. Where it says, "If you want to enter contributions to a Traditional or Roth IRA, follow these instructions," TurboTax is referring to ordinary personal IRA contributions. Keep in mind that if you choose to separately make an ordinary personal traditional IRA contribution, your SEP IRA contribution will make you covered by a workplace retirement plan.
