That's a tricky one, at least to me. There is a special address that you send the W-7 along with a paper filed, MFJ return, so I would say, paper file the 2021 with the W-7, and send it to the special processing center, would be the correct procedure. Of course, I can't remember the location, and it might have changed from the Austin, TX location that I think it was. Make sure you research what address to send it to, because if you use the wrong processing center, as I did, they will forward it to the correct location, which will create massive delays, on top of the backlog of unprocessed paper returns. Fortunately it was pre-Covid, in my case, so the delay was not too bad. Send it Priority Mail so you have a tracking number and delivery confirmation.

My client sent her original passport, which was part of the ID requirements then. Unfortunately, they both forgot a scheduled vacation, flights etc..., so now the concern was, would she get the passport back in time to get on the plane. Fortunately it showed up 2 days before their departure date, so just got lucky on that one. 

Once the ITIN is issued, I think it would be easier to file the Amended 2019 & 2020 because the ITIN would be in the IRS system, thereby easier to verify on their end. I think filing the amendments before the ITIN is issued, even with all the backup documentation, would just cause the IRS to reject the amended returns because they would have no method to verify the ITIN and they would not take the steps to verify you sent it to the special processing center.