The Foundry really doesn't seem to be much more than an afterthought for STO production. I'm not sure there's any real reason why they couldn't promote the missions to official status (although in doing so I think they would have to take any further modifications out o the author's hands). I just don't think they even spend more than a pittance of time even thinking about the Foundry.
In a way I'm not sure we'd even have the Foundry at all if its development didn't coincide with what was needed for NWN. Maybe I'm being overly cynical, but lately the only Foundry updates we've received have certainly been due to Neverwinter production.
I do think it would benefit STO if the best missions were at least made semi-official with specific rewards given, as the game lacks content. They wouldn't be official canon, but their play would be a little bit more encouraged.