I've only skimmed this but there seems to be a focus on customizing and plugins from the get go. I think it's worth getting to know Vim "as is" before doing such things. Indeed there certainly some things that aren't the most useful or obvious but it's good to understand their original intent.
Not to crap on the author of this but I'd recommend Drew Neil's Practical Vim over this (and pretty much every other Vim book).
I kind of agree but vim's defaults are awful. Tim Pope has put together a good set of non-opinionated defaults which don't change key bindings or customize it otherwise [0]. I have a very similar vanilla setup with no plugins apart from syntax highlighting for some languages not included by default.