all the solutions i have for the hair problem have been terrible so far. the problem really is that topknots poke out of the hats and helmets. someone had a way of preventing the hair from being rendered when it poked out, but it caused really ugly problems with the shaders and even caused non-hair objects to become invisible if you looked at them in certain angles.
one solution would be to model hairs with the helmets themselves, but it'll get weird since bald people will instantly get hair and blondes will instantly get black hair. but no matter -- those particular hats you posted plus hachimaki will probably be fine with hair enabled because they lend themselves well to topknots unlike the sugegasa and jingasa
as for the religion system -- both individual characters and whole clans can choose to have a specific religion or to be non-religious. the different sects of buddhism and catholic christianity are among the religions that can be chosen. shinto will obviously be present, but it won't be something you can "choose" because it had a complicated status before the separation order of 1868 -- it will be treated as a folk belief system as opposed to an organized institution that can raise armies and wage wars. protestantism might or might not be present, but it won't have a lot of features because it wasn't a missionary religion in japan -- it would be a flavor thing so you could more immersively play as an anjin miura-like character
the way i intend to have the ashikaga shogunate and emperor set up will be that you can't really interact with them until you gain enough rank, and you won't be able to do much for them until you first take over kyoto. once you do, you would then have two options available -- support one of two ashikaga heirs to become shogun, or to support the emperor (whereby you could either become kampaku like hideyoshi or shogun like ieyasu). by "support" i really mean "puppet", but if you piss them off enough they will assert their independence and bring other allies against you
there's also a third option of the status quo (such as with the miyoshi, the hosokawa before them, and the matsunaga afterwards), which might be the only one available if you're not powerful enough.
once you've chosen the ashikaga or emperor option, you will then have to do quests to pacify kyoto and fight off an alliance of clans that will try to destroy you. the difference between the ashikaga and emperor options is that the ashikaga option doesn't allow you to be shogun or kampaku and will eventually limit the amount of conquest you are allowed to do, but will be an easier path. the emperor path potentially gives you more power, but will be much harder. at any point on the ashikaga path you can move over to the emperor path
