https://github.com/revanced/revanced-manager for YouTube (and other App mods), you need to patch the app yourself. (If you are downloading a patched apk you are getting scammed. You have to patch it yourself) https://github.com/mihonapp/mihon for manga / manhwa I use internet archives for paywalls but their might be a better solution. F-droid has a a lot of neat open source app, I guess you know of it since you are picking graphene, but just in case. Firefox supports addons, it's been a great browser (though its UI is a bit rough sometimes) and could be your solution for YouTube with uBlock and the background play addons. I personally don't like graphene launcher, I personally use NovaLauncher (the paid version), their is quite a lot of FOSS ones too.

edit: sorry for the formatting, my phone f it up