"Does contributing to the SEP IRA effectively create a deduction from income such that the stock sales would be treated as "pre-tax" contributions?"
Yes. When you make a SEP contribution as self-employed, the contribution appears on Schedule 1 line 16 as an above-the-line deduction. This deduction makes the contribution pre-tax. Of course any SEP contribution that exceeds the maximum permissible contribution is not deductible and is subject to penalty.
