What difference would it make if he had Isabella as a 13 yo? He'd be what, about mid 30s still? Not a big difference, I have a brother that is in his early 40s can't say he was really any different in his early 30s. Also his profession of police... doesn't bring maturity, unless you failed to notice corrupt cops exist, or assholes on a power trip, being a cop require training, not emotional stability, many cops aren't there by any mean for their mental fortitude.
As for the MC being a mess... well yea... that is the point, he is clearly suffering from arrested development, his relationship with his Mom which was early on very erotic & even sexual and him effectively having to be keeping her afloat amidst her issues, his relationship with Amber with her being in a way dependent on him due to their father being an asshole and their mother being a mess. His girlfriend with her whole lot of issues, abandoning him shortly after having given birth to their kid to go avenge her father figure.
Do you really think the MC is sane by any means? No he isn't. His girlfriend choosing vengeance over him, and him going after her over his own daughter, he clearly has stalled emotionally at that stage for nearly 20 years. He clearly also to some degree fled from home, probably to escape his abusive father, and fleeing his complicated relationship with his mother and sister.
Oh and what you mentioned for it working for him being an inexperienced mid twenty with a heart broken... that is exactly the point, he never moved on from that, he had sex with 3 women as a teen & young adult, his Mom, his sister and his girlfriend, after which point he kept looking for his girlfriend for nearly half his life, having possibly only sex rarely on the side time to time to take the edge off but never moving on and getting into any serious relationship until Arlette. Which took him about 17 years to happen... so yea he is still an inexperienced young man at heart, sure it seem shortly before the story begin he might have had a bit of a breakdown and went on a sex binge with several girls / women of various ages, but that didn't bring him any experience in actually dealing with women, it was just sex, at most it just mean he hit 'College' level of emotional development.
I mean Amber is hardly better, she should be in her mid 30s and she is a sexy streamer and behaving also like someone in arrested development in her early 20s... Isabella basically jumped on her father as soon as he came back in her life trying to claim him for herself and jealously trying to keep other girls at bay, Madison had to raise herself because her mother spent her time drunk and without her son around she likely spent most of her time completely lost, and her father was probably just as neglectful and abusive as he was to 'his' first two kids, her sister was likely emotionally absent because she kept also like their mother clinging to her missing brother, also likely had to compete for what affection her mother and sister had with her niece / sister, which probably won because she was the daughter of the missing son / brother, she mostly end up acting like someone that had to grow older than her actual age because of that, and because of that she basically learned to be manipulative to get whatever she wanted.
So yea Madison's relationship with her 'brother' and likely actual father if you pay attention to the fact their is a scene where you see the MC had sex with his Mom as a late teen while she was drunk, is built upon her behaving like a mature woman manipulating a young man, because emotionally that is where they are at, he didn't mature in 20 years and she matured in acceleration. The MC ultimately is reacting to her as normally a young adult would to a very dominant mature woman, its all understandable within the context of the story.
As for his appearance, well one thing to remember, this is all happening in Japan... have you EVER read, watched or played anything out of Japan? I assume you haven't otherwise you'd realize they have some pretty different cosmetic standards to our own. So while yes he looks peculiar, its not really shocking due to the where its happening, sure the MC and his family are Westerners, but all living in Japan, so likely they have taken to some degree to their mindset.
Well I'd say it did some good amount of added content although some of it got removed to, or has yet to happen. Mostly the intro part has been significantly expanded so we get a better idea of what the MC has been going thru the last year or two before the train, it develop his relationship with Arlette, so she isn't just some mysterious woman anymore, you can tell she was his second significant romantic relationship after his girlfriend fucked off, after like 16 or 17 years being alone. It also show him fucking around more than previously shown in that chaotic period of like 1 or 2 years before the train.
It also change some of the way some characters are acting, Madison and Amber aren't as antagonistic anymore, Madison and Isabella as well as Isabella and Nanami seem more distant. Amber seem at first more distant to the MC, but get back closer, also their relationship seem a bit nicer and less just carnal. Also I think Amber gives less the impression she was somewhat promiscuous while the MC was absent and instead she is a sexy streamer, so she gives off a more youthful vibe, sexy yet chaste than previously, where she felt like she was a mature seductress.
