You're welcome.  That's what this forum is for, sharing info. 

The funny thing was that IRS rejected the extension e-filing for the S corps, for the very same reason.

I also had a June 30 YE exempt org that paper-filed its extension in October 2020, filed the tax return in March 2021 (before the 5/15 extended due date) and got a late-filing penalty notice in less than three weeks after the e-filing.  Three rounds of explanation letters and phone calls were made (due to the computer generated past due/collection notices.)  Finally got the penalty reversal letter in early October.... 

In any case, I'd call it amazing that the IRS is still somewhat standing after processing the three rounds of EIP payments.  That volume of work...  It's not just COVID per se.  I tried to paint the picture to the three S corp clients (and the exempt org).  I didn't really want them to incur such high fees for filing the dog and pony (rather time-consuming)1120S, but it is what it is, and I imagined if they had not paper file the 1120S on time, the $xx per-month penalty would stack up once the F2553's were processed and "approved".  I ended up not charging the exempt org for the penalty waiver letters and the calls. 

What a crazy tax season!!