Microsoft puts compatibility features topmost and that is the reason for multiple ways to do any thing. Sometimes I hate it, but if I think about it more clearly its a big asset to know that stuff you know will always work on Windows even if it get 'deprecated' by newer stuff.
IMO, you should learn to do any Windows configuration with PowerShell. You will have consistent interface for everything and as additional benefit you will learn shell very well and can bring it on with you to *nix world.
Regarding books, Windows internals is great one but probably not what you seek (mostly low level stuff). Sysinternals stuff generally is great way to understand and dominate Windows.
https://www.microsoftpressstore.com/store/windows-internals-...
Windows evolved across several generations of PC technology dating all the way back to the original 8086, major shifts in consumer expectations, and major shifts in vision in the leaders who managed Windows development. Windows is successful because it evolved to fit its role and Windows is also messy because it evolved to fit its role.