Sorry for the late response.
I'd recommend including the modlets for a server. I do eventually want to add in a hook to the mod launcher where all you need to do is provide a list of modlets to install, but this probably wouldn't work for you and your server.
While your server will push the XML changes, your clients could have new version of the modlets, courtesy of the auto-refresh of the modlets. This means your clients could have newer versions of the unity3d bundles than the server does. That in itself isn't a problem, but if they change names inside the bundles, remove, or add stuff, etc, it'll cause confusion and random errors.
The Mod Launcher knows how to copy key folders over. Data, Mods, etc. Replicate the game structure in your zip file. If its not in the right places, the mod launcher will still try to manage by coping based on filename matches. So if you have windows.xml randomly place, it'll find that file, find a matching file in the game folder, and copy it over.