
Well, I read a little of the spoilers on the "relationships" that come to near the end.
Small Spoiler and the couple spoilers in the last section below.
Safe to say your thought process is in the right direction, the ones who end up together mind-boggles me, and learning who Jupiter was and what our MC was even more mind-boggling. If you want to know that, let me know, it was a really strange mess.
He ends up with Elle, they have a kid. Jupiter ends up with the Demon King chick and this is where I'm confused since someone says they have a kid while another person says they don't, oh well. MC's Mom and the director marry [no surprise there, we saw this coming for a long time] and have a kid. The kid parts were in side stories I heard.

Ah about that...
Jupiter is none of the above. He is the child of Gaia's that Cronus of the other timeline had experimented on. Our MC was just a vessel made so that her son could be born. Since she is the system, she made it so that her child could get another chance at life and put him in our boy so he grows alongside him none the wiser. There was good reason for Lucifer to be cautious around Jupiter because he was the child of Gaia.
It's a bit of a mess there, Cronus is 100% trash.

I didn't look too into it, wanted to have some things to look forward to reading. I assume Jupiter isn't strong enough yet to separate. My theory is he might need to take in more of something to leave the MC's body. Looking back when the two dueled on the 50th floor; it felt like if the MC lost then Jupiter would have possessed his body, but seeing how Jupiter lost I'm led to believe he'd co-exist until he has the source to escape. Either that, or they'll have a body made for him and move his consciousness to that new vessel.
Won't know until the two separate. I like there being a little mystery on some events to keep ya coming back to learn. ヾ(❀╹◡╹)ノ~
Romance where lol there's only been implied crushes both between the ladies who crush on me to him on Elle but it's been a while I think it should be fine if they end up together.
Though Elle is one of those who keeps their feelings to themselves but explodes with strong emotions when stressed. I gather she probably has never experienced any feelings like this before especially due to her previous position within the angels, thus making her actions more expreme and harder for her to grasp that she is jealous and possessive.