Why is everything set to immutable and how do I reverse it?
The root user should always be able to change permissions on the filesystem. I believe things are made immutable by default to help avoid footguns by people who try to copy/paste things from the Internet. Requiring a root password may give people some pause, or at least give them the idea that changing files in /usr/local at random may not be a good idea.

Homebrew, the Mac package manager, makes /usr/local writable to be able to install packages from the web without needing to use the sudo command every time. It runs the following two commands to achieve that:

sudo chmod 775 /usr/local
sudo /usr/bin/chgrp "admin" /usr/local/&lt;unwritable directories/files below this&gt;