The path can actually be changed with a simple code edit.
XenForo_Template_FileHandler::__construct()
PHP:
$this->_path = XenForo_Helper_File::getInternalDataPath() . '/templates';
I can't say I'm 100% sure because it's been a while since I looked at it; but I'm pretty sure that's the only place it needs to change; because any interaction with the template files is done through that class and uses that path as the base path for all template files. Changing that, moving it outside of internal_data should do the trick.