I've been using calyxOS for several years on pixel hardware, and I'd honestly recommend you go with grapheneOS; it is technologically the more sophisticated project, and I've just sort of made my peace with the concessions I have to make using Calyx (it's kind of ideologically driven, given that I like the idea of microG in principal).
Genuinely I would avoid root on Android if security and device integrity is a key focus for you, but I also empathise with the perspective of wanting to feel like you own the device you paid for. It depends on what you do on your phone; If banking apps or the handling of any sensitive data fall into the equation, I would completely avoid root.
Similarly to you, I also used to block adverts systemwide via hosts / adaway. Today I use Firefox for Android with the ublock origin plugin. Any apps that would have presented ads to me otherwise have kind of been phased out over time by FOSS replacements (if there are any alternatives you need, please reach out).
For a comprehensive backup system, you might want to check out Seedvault? I'm not certain but I hope this will cover your requirements?
I'm not sure what 'mess with apps' internal states implies, can you please elaborate on this?