Do you really need such a plugin? It seems like a plugin that bypasses WordPress functions for the sake of security. Truth is servers are improving and WordPress as well. If you really need security, pick a very good hosting service and you are done :)
But yes, anyway, if you are using the client-method you don't have to put anything in the .htaccess, so you don't need to worry about it. And with that plugin I wouldn't go for sure for the server-method, I am pretty sure you will have issues.
One more thing: when you activate the plugin, it indeed "refreshes" the .htaccess. What it does exactly is that:
100% Through WordPress API, nothing tricky. If your .htaccess has an issue after that, it's coming from Bullet Proof Security.
I just discovered that they have a list of plugins that they support (and they have to support them one by one). Unfortunately it seems to be only the Premium version of the plugin...