.htaccess on multisite and roots theme?

Question

well, I have both roots and multisite. However, I do not have roots specific rewrite rules.

I have the vanilla rewrite rules defined in the docs. I use the ones for subdomains instead of subfolders.

RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# uploaded files
RewriteRule ^files/(.+) wp-includes/ms-files.php?file=$1 [L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule . index.php [L]

Comparing them to yours, perhaps, the bottom block is extra?