root or otherwise, you are not allowed access to /usr/bin and lots of other locations and operations which traditionally root had, in *nix. There is a way to bypass this (with something called "bypassing the SIP", not sure if you will ever be 100% root though!). Which I have not tried and do not recommend. Just get used to the fact that the notion of my computer is well behind us at least with Apple and Microsoft. To me, it seems their difference is that while MS trusts the security of its OS to illiterate IT operators brainmassaged sufficiently with """MS Engineer""" (top oxymoron) courses aspiring to that particular moustache style, Apple trusts no one but its own breed at cupertino.

I faced more problems, like code signing. And that homebrew does not support older OSX versions (and works 50-50 edit: for my 10-year hardware not allowed any more OS upgrades). And that you need that dreaded XCode for anything to be compiled. And the system becomes unworkable for the average bloke once the hardware's age forbids software upgrades. I personally use my old macbook for watching the occassional movie. And even that presents a challenge...

For some binaries, Homebrew refuses to install them in locations which shadow the system default. That's another caveat you need to juggle.

Q3: brew analytics off - though this is your least of the privacy problems as Apple keeps phoning home more than a butterboy in summer camp. (hint: pay Lulu a visit pronto and learn how to ban ip addresses using /etc/hosts)