Aha! Now I get it! The file remoteserver.dll which is the source of the web interface is actually made by Promixis who also make NetRemote! I'm now 100% sure we will never see a web interface for MC unless someone writes an entirely new plugin. After all, why would Promixis provide free functionality that directly competes with their $19.99 product... I also suppose this means the web interface should potentially be able to support all the functionality of NetRemote!
Since my last post I've also checked out Glissando, a Flash based interface for accessing Remote Server and although it looked pretty nice it used 100% CPU... It also seems to have been abandoned by its developer - and a Flash interface is not what I'm after anyway.
Some progress though: By using FileMon I've found that MC tries to access a styles.css file in the MC\Data\ foder. This file didn't exist on my system but by creating one at least I get basic CSS control over the font/colours used in the web interface. Far from what I'm really after but something to play around with at least.