Good points.
The vast majority of people in the forums seeking help who have multisite in /wp/ have their main domain as domain.com/wp/. Configuring the domain path to be in the root is another step that most don't seem to do. Also I would say 75+% of those people are using Cpanel.
I guess it's not really plugin related but rather a good point to include clearly in the documentation. Something along the lines of "if in the future you plan to map domains, make sure it's installed at the root of your domain." Etc.
Happy new year!