.htaccess and Managing Multiple Sites with Wordpress

I have seen article like:

Title: Multiple Sites with WordPress Network

As I like to use .htaccess on my own for all other parts of folders and rest of website, how is this integrated with Wordpress as this .htaccess can be overriden nd ruin all other Smarty based website pages.

Is this true?

The article talks about an environment of wp network. Htaccess file can allow or deny access to certain folders specified therein. I do not see how it can affect other non-wordpress sites.