I'm not sure we ever had to. On any of the sites we have (10+ domains) I can't recall having to make any changes to .htaccess from the defaults that wordpress uses when you alter the permalinks (excepting adding the Limit option in the httpd.conf file to fix a small issue)
I was thinking a smart workaround would be to do like wordpress permalinks do and show the code to add if the file isn't writeable. I can alter it to make it 777 until after caching is enabled if that helps?
By the way, still really grateful for the plugin. During the big attack on everyone a few months back it was extremely helpful to be able to show the business the graphics on your site showing all the bad requests and how wordfence was handling it. Also made justifying our multi-license purchase of wordfence to them :)
tim