I have used both, but not for touring -- for randonneuring. The trunk bag definitely has the advantage of being able to organise stuff into discreet groupings in the pockets. I am a keen fan of Topeak's original rectangular rack backs, although less so of their newer sloped-top ones. As for waterproofing, I think Topeak offers a cover rather like the ones used for their handlebar bags.

I used Sea to Summit bags to pack away a change of bike clothes and a sleeping bag on some randonnees. The disadvantage, as stated, is that to get to the stuff at the bottom, you have to take everything out. If there is small stuff in there, that brings up the possibility of dropping it and/or losing it. Another slight disadvantage is wear from contact points with the rack and straps/bungies that secure it. The distinct advantage is waterproofness without having to worry about an extra covering.

As I note in another thread, our touring bikes are equipped with the Topeak Tourist racks that have a lower bar for attaching the panniers. This obviously was designed to overcome the issue of trying to carry the rack bag and panniers together. By offering this rack with the extra rail, I can, if I want, leave a rack bag permanent on the bike and use it for commuting, leisure rides, randonnees or whatever, and just add the panniers without hassle when I need to. Mind you, that does present an issue with finding a place for the tent.

One other out-of-the-square thought is... have you thought of a Carradice saddle bag? You don't absolutely need a Brooks saddle to use one, and as Machka has shown in a number of her pictures, the Nelson Longflap she has fits quite well over her Topeak rack with the panniers underneath. And our experience with both our Carradice bags (yes, we have several, each) is that they are waterproof, roomy and durable.