No, the IRS will not automatically reject your return, and in fact, you are likely doing exactly what they require.
For CSRS and FERS pensions, the IRS understands the "Taxable Amount" in Box 2a of your Form CSA 1099-R may be different from the actual taxable amount you report.
Since your annuity started after November 18, 1996, the IRS requires you to use the Simplified Method to recover your "cost" (your after-tax contributions) tax-free.
IRS Publication 721 specifically states: "If your Form CSA 1099-R or Form CSF 1099-R shows a larger amount [than the Simplified Method calculation], use the amount figured on this line [the worksheet] instead."
TurboTax follows this rule by running the worksheet. It calculates how much of your contribution is being "returned" to you each month, which reduces your taxable income below the "Gross Distribution" shown in Box 1.
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