I have a working multisite wordpress installation with BWP sitemap plugin enabled to generate the sites sitemaps. (sub-folder mode)
It also adds the sitemap lines in the robots.txt file.
When the Multisite Robots.txt Manager plugin is enabled and the configuration is deployed over the network, the new robots.txt file does not contain the lines added by the BWP sitemap plugin.
It might have something to do with the plugin execution order but I didn't check it yet.