Found a solution for anyone who may stumble upon this. Basically, each part of a standard WordPress htaccess now has two RewriteConds: one for when it is in a subfolder, and another for when its not. Depending on that evaluation, the appropriate RewriteRule is applied.
# BEGIN WordPress
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
# add a trailing slash to /wp-admin
RewriteCond %{REQUEST_URI} ^/([_0-9a-zA-Z-]+/)wp-admin$
RewriteRule ^([_0-9a-zA-Z-]+/)wp-admin$ $1wp-admin/ [R=301,L]
RewriteCond %{REQUEST_URI} !^/([_0-9a-zA-Z-]+/)wp-admin$
RewriteRule ^wp-admin$ wp-admin/ [R=301,L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteCond %{REQUEST_URI} ^/([_0-9a-zA-Z-]+/)(wp-(content|admin|includes).*)
RewriteRule ^([_0-9a-zA-Z-]+/)(wp-(content|admin|includes).*) $2 [L]
RewriteCond %{REQUEST_URI} !^/([_0-9a-zA-Z-]+/)(wp-(content|admin|includes).*)
RewriteRule ^(wp-(content|admin|includes).*) $1 [L]
RewriteCond %{REQUEST_URI} ^/([_0-9a-zA-Z-]+/)?(.*\.php)
RewriteRule ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L]
RewriteCond %{REQUEST_URI} !^/([_0-9a-zA-Z-]+/)?(.*\.php)
RewriteRule ^(.*\.php)$ $1 [L]
RewriteCond %{REQUEST_URI} ^/foo/
RewriteRule . foo/index.php [L]
RewriteCond %{REQUEST_URI} !^/foo/
RewriteRule . index.php [L]
# END WordPress