For me I wonder if maybe Emi and Remelia in the end will end up as the couple? Like either Remelia will do something to seperate them or due to how they end the "storyline" they end up dead so go to the equivalent heaven together?
Cause it feels like Hidden yuri with how they both felt about the other personality.
Yes! This.
Look, if the setup involves two people revolving their worlds around each other and then growing that bond, feeding it, then those two have to end up as the main couple (or sisters in this case) or else nothing about anyone's motivations will make sense. Also, Remelia will never love anyone as deeply or as passionately as Emi, as Remilia will always know and trust Emi, Emi is her universe, Emi is what makes up her purpose. She knows every aspect of Emi, there is already an unbounded intimacy between the two, and Emi (if she had woken up) would learn all about Remilia, see how hard she's working for her, get to know the one who was inside her all along, how she supported Emi behind the scenes, cheering her on and the like, I think Emi has a decent chance of falling into further love with Remelia.
Though, I doubt the author would actually go into full-on yuri. It just wouldn't really make sense to marry your Goddess, would it? It's like being a nun at a convent, you're willingly and purposely celibate in order to dedicate yourself to God, not marry, dedicate.
But yuri would actually be nice. Remilia, in my opinion, would go for the 'living as sisters' option, sleeping in the same bed. It's been an established motive, and she probably cannot fathom being willingly further from Emi for more than a few meters. Not exactly all too different from being a romantic couple, but I don't think Remilia sees Emi in that way. Rem's probably like, a decade behind before she can really see Emi as a romantic interest for herself.
That doesn't make much of a difference however, as whenever Remilia would say 'I love you' to Emi, it'd have the exact same meaning, purpose, and intent as she would say it if they were happily married for the past century: Sheer adoration and cherishment of a blessing that makes up their entire existence and meaning.
Emi on the other hand, has more room for change. She, for one, isn't conditioned from her entire childhood and her life thereafter to being dedicated to just one person. And, if there ever were to be a yuri relationship, it'd come from her prompting Remelia to be lovers. As, it's unlikely within the next century that Remilia would ever see herself as... equals to Emi. Remilia lives her life for Emi, and only Emi. Emi lives (lived) her life for Remilia, and everything else that's good about the world. Emi would see Remilia as another person, a lovely one that she's fond of, but not exactly of romantic interest. She didn't know too much about Remelia's personality, who she is other than the lovely child who just wanted to be loved, to be given the respect worthy of a person.
However, this, this view can change. Perception is a fragile thing, and little things can shift things a lot, big things even more so. One of the smaller things, which may just be my headcanon, could be Remilia talking to Emi before sleeping, talking to her, making sure she doesn't feel so alone within herself. And if you're alone with one person, for a rather long time, a person that fearlessly trusts and adores you, a person who knows you well and does all they can to make you happy, not out of obligation but out of love, then... I'd say you're bound to fall in love?
Anyways! EmiRem best ship. They're perfect for each other imho.