Theres also the option that is wasnt him - as you point out yourself: It appeared to be Emet'Selch, but that doesnt mean that he was actually there. Just how Haurchefaunt and Ysayle werent actually there at the end of Heavensward when we finished Nidhogg off.
It might have just been our characters imagination or maybe some sort of subconscious "summoning" born from the wish to see him again (or something along those lines).

My personal interpretation would be that its not the Emet'Selch we fought and traveled with who showed up but more a... mental image our character has of him. And in that mental image, Emet'Selch isnt a fiend anymore, but an ally. This mental image doesnt need to account for him being tempered or not, because its not the real Emet'Selch - maybe its what we saw in him in the end, maybe its what we wish he would have become, maybe its a hidden memory of Emet'Selch before the summoning of Zodiark, tucked away in our immortal soul, maybe its our wish to part with him on better terms than killing him...
I'm just pretty sure that its not Emet'Selch himself - hes dead, gone for good. So whatever we saw in the end, its not the same Emet'Selch who was tempered by Zodiark and worked against us.