1. Schedule SE Part I provides the calculation of self-employment taxes and the deductible portion of self-employment taxes. (The only calculation change from the 2019 Schedule SE Part I is to the Social Security wage base, $137,700 for 2020.)
Draft 2020 Schedule SE: https://www.irs.gov/pub/irs-dft/f1040sse--dft.pdf
Chapter 5 of IRS Pub provides a clear, step-by-step calculation and is the calculation that TurboTax implements on its Keogh, SEP and SIMPLE Contributions Worksheet. Even if you don't understand why each step is present, following the steps as indicated will lead to the correct result.
2. I'm not sure how a self-employed individual would ever not be in-service. eTrade is probably indicating that distributions are NOT permitted from the plan before age 59½. Certainly the law prohibits in-service distributions of employee elective deferrals and Roth contributions from a 401(k) prior to age 59½, but it's up to the plan to determine whether in-service distributions of other amounts are permitted before age 59½. An In-plan Roth Rollover (from the traditional 401(k) account to the Roth 401(k) account in the same plan) is permitted by law at any age but it's up to the plan to either allow or disallow IRRs.
A 401(k) is not an IRA. Form 5498 only applies to IRAs.
3. Contributions to a 401(k) are not IRA contributions. A nondeductible contribution to a traditional IRA would be made to a traditional IRA, not to a 401(k).
