For me I'd never use mdf. Too many horror stories that I've heard and have actually seen for myself. I'm just wondering if the ply could be of the same thickness (0.8/9mm) as the ply timbers from the Scale 4 Soc stores or perhaps thickness of the timbers could be a customer option? Just so that the transition from one system to the other wouldn't cause any problems. As for ballasting - I can't see a problem with the webs, most - if not all - will be hidden by rail. Having seen the way Norman Soloman adds his ballasting to track, it certainly won't be a problem. Just my thoughts.
Mike