There currently aren't any filters to help you get done what you need but it's an idea for the next release. That means you'll have to modify the plugin files themselves. But, next time I release an update it can overwrite your changes if you upgrade so you'll want to make a back-up of any changes you make.
In class-plugin-mncombine.php, line 800 starts the loop to combine/compress the files. The variable $data stores the file info. You could inject the data of your external files there. However, lines 804 to 807 check that the file exists locally so you'll need to conditionally skip those lines for those files.
Pretty much the same thing needs to be done on line 1053 where I loop the css. Hopefully from there you can figure out a way to code in the external scripts. Obviously this will be much easier if I had included a filter.
I have not tested with a multi-site install. The plugin searches for the files that belong to the active theme and not in for files in other themes so that could be why some work and others do not in a multi-site environment.
Good luck, let me know what you come up with!