I've beat the game every way possible and absolutely loved it. I know the couple that you're talking about but can't remember much else about them to be honest.
As far as the Embers quest goes, feel free to do it whenever you want. Once you beat the game it spits you right back out in front of Embers so you can continue doing all the other stuff. You also get to keep all the cool stuff that you got doing the end game.
I've beat the game every way possible and absolutely loved it. I know the couple that you're talking about but can't remember much else about them to be honest.
As far as the Embers quest goes, feel free to do it whenever you want. Once you beat the game it spits you right back out in front of Embers so you can continue doing all the other stuff. You also get to keep all the cool stuff that you got doing the end game.