Great write up James,

This is a huge topic and you've done a solid job of summing it up. Congrats. One quick correction you may want to make is in the statement:

The mu-plugins category is THE place where we get to globally define what’s happening for our sites.

As you point out below this sentence, the mu-plugins is a directory under /wp-content/ and not a category.

Just trying to avoid any confusion for those new to Multi-Site...