I agree. There is a lot of "magic" going on, and it doesn't help that Spacemacs is a lot slower and less stable than my less-intensive personal customization.
Of course, that's the problem with any significant starter kit. As a new user, now you don't just have to learn emacs, you have to learn emacs + whatever heavy modifications they've done to emacs.
In principle, I liked Spacemacs, but stability is a big problem. Often certain org functionality stops working, etc. I now have a reasonably stable snapshot and I just don't update ELPA/MELPA packages anymore, because the risk is simply too big that things break (yes, I know that you can rollback).
Another problem that I have been running into is that Mitsuharu Yamamoto's emacs-mac, which is IMO by far the nicest Mac version regularly seems to trigger a bug where WindowServer starts using 100% CPU. I haven't really nailed it down (I only notice it later when the fans start getting loud), except that it only occurs sometimes when I run emacs-mac.