LPCP doesn't do any .htaccess mods. At least none that I've found.
Really? Are you saying that it won't do anything that simply edits the
.htaccess file (e.g., turn indexing off, do redirections/URL rewrites, etc.)? If so, maybe they just saved that for last (low priority), as it's just a convenience feature rather than something that a site owner absolutely can't do on their own. I.e., the site owner can always edit
.htaccess and directly add commands, although most would prefer to let the control panel do that.