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I've made some modifications to my TeX installation outside of the TeX Live Utility, which I use primarily, as a convenient way to keep my installation up to date. For example, I've added some fonts manually followed by texhash, and some others using getnonfreefonts.
Does that mean that after each time I run TeXLive Utility (or tlmgr), I need to rerun any and all other config tools I might have used outside of TeX Live (e.g., texhash or udmap)?
If you install fonts in the "local" tree (/usr/local/texlive/texmf-local) then you'll run updmap-sys for making them known to the system and no intervention should be necessary in case tlmgr updates font related packages.
The getnonfreefonts-sys tool just does this automatically.
The situation would be very different if you installed fonts in your personal tree (~/texmf on GNU/Linux systems or ~/Library/texmf on Mac OS X) and made them known with updmap (or you used getnonfreefonts).
In this case changes made to the system wide font map would not be reflected in the personal font map that updmap has created. Therefore it's always best to do "global" font installations and updmap should be run each time an update to TeX Live acts on font related packages.
texhash I assume, as long as I put them in /usr/local/texlive/texmf-local?
mktexlsr (the real name of texhash is automatically performed by tlmgr after any update and it acts also on the local tree.
If you installed your fonts in TEXMFHOME, check the box for "Automatically enable fonts in my home directory" in TeX Live Utility's preferences, and it will run updmap for you after an update/install.
$TEXMFLOCAL.