I found the place to enter adjustment: To reduce the self employment tax in this case edit the SEP IRA worksheet ("SEP/IRA Wks"), override line 2b ("Adjustment to self-employment tax (for adj to net earnings)"), and enter the correct negative number that would fix the contribution limit. Explain in the automatically created note. After this adjustment TurboTax automatic calculation always shows the correct amount (even if you recalculate).
