.htaccess files are folder specific, I am sure it creates stuff that's ideal as far as Apache security is concerned, but above/beyond that, a secure site would not allow most of the rules to work in .htaccess files in the first place. The thinking is that if a plugin could write .htaccess files, than so could any other process that could run by the web server, which in-itself is a security problem. If this security plugin walks you through setting the file permissions to these .htaccess files after it generates them then that's better, but still not ideal.
I understand though that economics plays a big part in being able to afford a full time administrator or paying a hefty dime for web hosting that has security measures in place. I'll look into the plugin conflict at some point soon.