No 404 on existing folders

I'm really out of ideas. Generally, I would try to see if it makes a difference to remove the RewriteBase when it's in the subdomain, and maybe try to see if it works when you replace your current RewriteRule with a more common set of rules. I know that most of the rewrite configuration on my server started with the .htaccess code in Bonfire, but I've had to make modifications for almost every environment.

Bonfire

Practical CodeIgniter 3
CodeIgniter Testing Guide