Critter - I think you mis-understand. Tax return transcripts always only reflect the information provided on the originally filed return. Amended returns are simply processed as adjustments to the originally processed return on the account transcript, they don't actually change the return in any way. This is true even when amending from a sepate return to a joint return, which I wasn't sure about. I did not file a separate return before amending to a joint return because I would have owed interest, penalty, and late filing penalty as opposed to just amending the spouse's separate return to be a joint return and get a refund, and that did work! (but they surely did begrudge me for it!)
What I was reporting is that when amending a return from separate to joint, and the other spouse never filed, IRS associates the one separate return being amended as the originally filed return with the non-filing spouse. I guess that is necessary and sufficient to mark them as filed on IRS systems, but it still isn't their separate return and doesn't show their name, income, or taxes at all! Kind of weird seeing spouse's MFS return as my MFS return also, and certainly could cause great confusion if I needed to give a tax return transcript for income verification, but that's the way they do it in this case.