SPOILERS
It's interesting that you mention those parts as being surreal! For me when I was writing it, the parts where MC (clones and OG MC) is monologuing while inside the chamber during the hidden route were most surreal (because the music for those scenes just made me feel strange xD)
I'm glad that you enjoyed the softer, more romantic moments too :3 It was really difficult for me to tell if I had written them okay because I enjoy writing the darker stuff more, haha. I wanted there to be those bittersweet moments between them though to show just how in love the pair were/are <3
In regards to unlocking the hidden route, you don't technically have to see every single bad ending to unlock the hidden route :3 I can't even remember exactly how many bad endings there are now xD and not all of them have CGs. But I set the unlock requirement for the hidden route to be 5 or 7 less than the total amount of bad endings I think. There is also a bug/exploit which I kept in the game because some people were having issues with the way I've done the points and the save system. So the exploit is that you can view any bad end multiple times and it will still count towards the total needed to unlock the hidden route. You can technically just watch one bad ending 30 something times and unlock the hidden route to play x3
With the MC traveling back in time in the hidden route, like a lot of stuff in the hidden route, I kinda left it open to player interpretation on purpose because I didn't really want to just pick one absolute truth and tell people this is exactly what happened (I'm a terribly indecisive person, haha.) Some of the ways I was thinking it could be interpreted are:
1) Like you said in your comment, it could be part of solipsism, so the MC decides that she doesn't even have a way of proving what is real and what isn't, but instead of letting that upset her, she just accepts that her reality is whatever she is currently experiencing. (This one is the one I sorta had the MC talk about at the end, but it doesn't necessarily mean it's the absolute truth.)
2) Or like you said in your comment, it could all be part of Anathema's mind!
3) Another way you can look at it is just that simply none of it was real at all, and it was all just in her head. OG MC is the only thing that truly exists, and everything that happened was just part of her own imagined world... but that's a bit depressing x3
4) Oooor, you could even just say that Isaac's experiments were so successful that he created a superhuman who can actually control time somehow, haha.
There are probably more, but I have some brain fog at the moment so I can't think >.<
As for the relationship statuses of Raine, Isaac, Lilly, OG MC, and S****, I didn't really go into much detail in the game about their backstories and how everything came to be just cos I thought people might get bored if I did too much of a lore dump on them x3 I never actually gave any of the characters definite ages when I was writing, but you're pretty much right in what you said.
When the world was normal, Raine was in a relationship with MC's dad, who we don't get to hear about at all in the game, and Isaac was in a relationship with a woman who would have been S****'s mum, who we also don't get to hear about. At some point, they would both have lost their partner's in some way. Raine and Isaac were both scientists, so would have ended up meeting through work, and then MC and S**** came to meet and became a couple before the world went to shit. At some point, Raine and Isaac would have been good friends (possibly on/off lovers.) I kind of like to think that Raine had Lilly some years before everything went to shit. So Lilly would have grown up around MC and S****. It probably would have been quite a weird situation for her like you say, to know that her half-siblings were a couple. She likely would have felt somewhat left out and easily jealous. I like to think she was a teenager when everything went badly on the surface and they all had to go underground. I never specified how many years they were all stuck down there, but it would have been a lot. So Lilly would have done most of her growing up in the lab, separated from her half-siblings and manipulated by her dad.
I always imagined that S**** was older than the MC + that Isaac was older than Raine. Lilly would be a fair bit younger than MC and S****. Everyone in lab is older than they look though because they were using various methods to stay alive beyond natural means (like S****'s artificial implants Isaac made for him.)
As for how OG MC and S**** met, if I'm completely honest, I don't know x3 I had never really given it much thought before! When I was writing the story, I just kinda knew that I wanted to write about a couple with a bond that was so strong they could survive crazy amounts of hardship. So I just sorta thought of them as always having been in love, kinda like destiny pre-dertmined it, haha.
I never really gave it that much thought about whether S**** has a bit of a possessive streak like the Kuro's. I think that he probably has the capacity to become like them under the right circumstances, because at the end of the day, MC is the most important thing in the world to him, and I don't think he'd ever give up on the idea of being with her. We don't see what might have happened had OG MC rejected him upon waking up... that could be an interesting alternate route, haha. I was tempted to put a choice for something like that in there, but I decided I couldn't do it, because there was already so much suffering in the game, and to me, OG MC would never reject S**** so I decided that the player wasn't allowed to make any choice about their relationship, haha. I think it's possible he could snap in that sorta situation though!
There's no need to apologise anyhow :3 I don't mind answering questions + it's nice to discuss the game! I'm just happy that you enjoyed it so much <3