None of the SEP contribution gets counted in the nondiscrimination testing, so the amounts contributed to the SEP count as a zero EBAR and fulfills $0 toward the minimum gateway.
I wouldn't typically terminate a plan before the end of the year if the company wanted to make a contribution for that year, or else, as Bill Presson notes, you do something to waive last day requirements or whatever. Depends on what you want to happen I guess.
mutatis mutandis to you too.
If it's a safe harbor 3% nonelective plan, I believe EPCRS says to use 3% as the makeup QNEC. (Looking at page 85 of 140 in RevProc 2021-30 while typing this)