This is a very good point. I first tried to jump in Emacs by using Spacemacs, and was overwhelmed trying to manage the fairly huge and complex init.el that Spacemacs produces. I also had lots of trouble before realizing that Spacemacs and vanilla Emacs package configurations should really be treated as separate and not mixed together.
I'm sure if I went back to Spacemacs now, I'd understand things a whole lot better, but as a new user, it was far too much to figure out at once.
So I went Vanilla, and haven't looked back. I do think that there should be some more articles out there like "so you've decided to try Emacs? Here's what to do beyond opening and saving documents". With a heavy emphasis on, as you said, incrementally adding to your configuration. Something like "here's why you split your config file into 2, with automatic changes going into one file, and manual going into another" followed by "here's use-package" and "if you want to X, here are Y packages that do it" with comparisons between each different way. But broken down into small chunks so things can be done incrementally.