@givemersspls
Some stories just go with it without any explanation.
Like Kyoko-chan (https://mangadex.org/title/12900/fudatsuki-no-kyoko-chan) it's never explained on how he got a Jiangshi sister. It's pretty common for comedy and slice of life IMO.
1. INCEST
Well, first of all, girls mature faster. Back in elementary school the girls was all about dating boys, while the boys just wanna play their Tamiya. And... Nothing weird. Her crush, who supposedly only lives with his mother, suddenly live with someone their age, and he obviously hiding and lying about some stuffs. So I cant see what's the incest part here. Forget her, if my own friend suddenly had cute girl living in his house outta nowhere we would tease him for it.
2. MALE FRIENDS
Do you know the term of "side character"? The main story here is about the daily life of him and his mother. It's just like Dekisugi in Doraemon. Dude is the main love rival of Nobita and barely appears, but he is still there. And yes, my male friend would be, in your term, 'extremely marginalized' when they are not related to my business! Why the hell would my male friends popped outta nowhere when I'm shopping with my mom for example? You want 1 volume of him playing with his male friends? His male friends appeared pretty much in all school scene.
3. CHERRY PICKING
Anyone can see you're the one cherry picking. I explained it as a whole in simple sentence. Which is "this is pretty normal grade schooler life except for the part his mom turned his age".