If I e-filed a 1099-MISC(NEC) late one day, on Feb 1 and did not submit an extension Form 8809, do I still submit the extension request now?

No, you don't want to confuse the IRS. 

If they send you a penalty assessment which is doubtful, you can request an abatement/waiver of the penalties using the instructions and Form 843, Request for Refund and Abatement at the link below. 

I would wait until/if they send you a bill first.

https://www.irs.gov/uac/form-843-claim-for-refund-and-request-for-abatement