Hi James, and Welcome,
I used 12 mm ply for my T2, and like you had alot of rubbing and filling to do before getting a smooth finish.
I am currently building a 1/2 scale 'Mini Moke', and am using both 12 mm ply (for the Inner Panels), and MDF for the 'High Finish' panels.
I would warn you that, although the MDF gives a very nice, clean edge, and is easily worked with either sander or router, if you drop any of the MDF panels (as I have done on several occasions), you are very liable to damage them! This manifests itself as a 'Flairing' of the board, especially if dropped on a corner!!

I have found 'MDF Sealer' in my local DIY shop, and intend to use this first, then cover the panels in slightly diluted PVA, in an attempt to seal any moisture out of them.
I (personally) wouldn't have thought that moisture would be a major problem, once the body tub is painted in it's gloss 'Top Coat', asd this should provide adequate protection.
Providing that you don't get the panels soaking wet, minor moisture (in the air) shouldn't trouble you unduely.
Hope this has helped you.
Keep Busy,
Regards,
Mark. (resident nutter)