Thanks for your interest in the plugin! Others have reported that things work fine with those directives in place, so if they are working for you, just leave them there.
That being said, if you run into any issues, I'll ask that you remove them before I can help troubleshoot things.
It looks like the WP Multi Network plugin you linked is a copy of my original Multi-Site Manager plugin from the WPMU days, updated with the new "Sites" for blogs and "Networks" for sites naming scheme. So, the plugins will be similar since they come from the same source. :)
Networks for WordPress has been updated with support for WP 3.1 and better use of the "Network" name feature, along with some better documentation.