"in Proseries for Form 2210 Line 2 in the 2020 software says "From Schedule SE, line 12 minus line 26....""

"I was surprised when I read the IRS instructions for the same line it nowhere says to reduce by Line 26 of Schedule SE."

Here: https://www.irs.gov/pub/irs-prior/i2210--2020.pdf

Line 2
Enter the total of the following amounts.
IF you file... THEN include on line 2 the amounts on...
1040 or
1040-SR
Schedule SE (Form 1040):
Line 12 minus line 26,

And then, for 2021 safe harbor lookback, to  confirm enough Est was paid in for safe harbor, there are lots of additional adjustments and provisions:

https://www.irs.gov/pub/irs-prior/i2210--2021.pdf

Line 8
To figure your 2020 tax, first add the amounts listed in (1) below, then
subtract from that total amount the refundable credits listed in (2), later,
that are shown on your 2020 tax return

What I see is the mixup of tax year.

For 2020, the amount that should have been paid in for safe harbor is adequate as long as it works with the math of current year/prior year (standard safe harbor provision) Total tax owed minus the SE deferral provision amount, even if not using that option.

For 2021, the only issue is to figure the amount that safe harbor would be based on, not reducing it for SE tax (which was owed and just the payment was the deferral), and adjusting for the various credits that would not be part of 2021.