It doesn’t help that the guidance is contradictory as to what to do. An accountant that told you to do either would be right. Some states take a hard stance on this, though.
My general view is that there are several ways to file things that are accepted by the IRS but not on the forms as written. All 9s, NRA, declaring 1 as interest income if you have 0 in order to file, etc. those are workarounds that the IRS permits as they don’t materially impact tax, but the standard is to follow the form as written. 99/100, this type of thing doesn’t matter, but we’re dealing with the 1/100 where it might.
Rather than argue about the theoretical here, it’s best to look at what would help OP. An MFS filing as NRA wouldn’t help OP for immigration purposes as it doesn’t show joining of finances. It also could hurt them for tax purposes, and they’d need to amend again once their spouse is here to get MFJ. There’s really just no benefit to the MFS status for them at all at this point, and it’d be better just to wait to amend.