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The documentation actually says to use M-x customize-group (not configure-group), which is the builtin UI for accessing customisation options exposed to end-users.
In the end though, my config now reflects a much better emacs experience for my personal use, and I actually understand what it’s doing. I learned a lot along the way, and most of those lessons have helped improve the way that I use emacs in general. I do maintain a copy of my config on GitHub although it’s probably not a drop in solution, I don’t imagine anyone will be using my config so I haven’t gone out of my way to make sure it works out of the box for anyone but me.
For the which-key thing, it is in the doc under section: "Keymap-based replacement". https://github.com/justbur/emacs-which-key
I used spacemacs for about a year before giving it up and going my own way based on similar kinds of frustrations. I found it relatively easy to pull out (or use as inspiration) the parts of spacemacs that I liked. You can see the current version of my config using evil and space as leader here. I think Doom is good, but I like maintaining my config and found it unnecessarily complicated for what I needed. YMMV. I'm actually in the process of simplifying my config now with features from nano-emacs and using icomplete-vertical/consult/embark. We'll see how that goes.
Wrt customize API I recently had this interaction with Doom's author: https://github.com/hlissner/doom-emacs/issues/3926 and they say they'd rather not have people use customise because it clashes with their stuff in some hard-to-fix ways. Customize is more than just setting variables, some settings have associated code that runs. I personally avoid customize too, because the way it saves config is just a flat sexp that's hard to VCS properly or fix manually when need arises. The author also says "Doom was designed to be keyboard-centric and targeted at experienced users, rather than beginners (though, admittedly, it attracts beginners in equal measure)", which IMHO is an important thing here: Spacemacs and Doom are very sophisticated Emacs configs, so they probably work better for experienced users who can comfortably debug Emacs, profile it, and work things out where docs are scarce.