You'll have to ask Waterford the significant differences between the two bikes but I believe that the only significant difference is geometry. Since all Waterford's are custom, you can specify tube thickness, which is probably slightly thinner and "livelier" on their standard RS model.
I ride an RST-22 and I wanted it primarily for commuting, long rides, and light touring. More info can be found here - Waterford ultimate commuter, with pics
Let me see if I can tackle your questions, but as a previous poster mentioned, you'd be best of just contacting Waterford and asking them, they do build bikes for a living and they aim to please their customers.
1) In general, the TIG-welded R-33 tubing is going to be stiffer and slightly lighter than their lugged frames and even OS & OS2 TIG-welded frames. If power transfer, counting grams, and responsiveness matter most, you're best off going with the R-33 tubing. If comfort matters most, you're better off with their OS2 tubing, either TIG-welded or lugged, the difference is largely aesthetic.
A) An RS is going to be best for club rides if your rides are moderate to fast paced but an RST would do fine for more casual rides. The RST would probably do fine for moderate and faster rides too, the difference is more in the rider than the bike on most club rides I've done. The more upright you are, the less power you can generate and that's less a function of frame materials than the geometry of your bike, which is completely customizable.
B) The RST standard geometry is certainly more comfortable in terms of fork rake and top tube length. As others have mentioned however, Waterford's are fully custom so this is a bit of a moot point. Tell them what kind of riding you'd like to do and your other parameters and they'll suggest a good geometry, based on your measurements.
C) A bike that's going to be good for fast club rides isn't going to be as comfortable for long weekend rides and credit card tours. Unless you really want to sacrifice the lively feel of the bike on a club ride or even a century, you're never really going to be able to put any sort of load on the front of the bike. Any bike meant to carry a load on the front wheel needs some drastically different tubing and geometry than a bike designed for fast rides. If by credit card touring you mean 20-30 lbs. on a rear rack and maybe a small handlebar bag, then you can get away with this "club tourer" you're aiming to build. And here, an RST is much better suited than an RS, the latter of which would get a little squirrelly under load.
D) Handlebars level with saddle is pretty easy to do when you have a custom build like Waterford. I left my steering tube pretty long for this very reason and like the flexibility I have with spacers and handlebar placement. Waterford is generally very accommodating to your desired saddle vs handlebar height and if you're set on a TIG welded frame, this is a breeze. A horizontal top tube at your height might not be possible however, I just don't know enough to comment.
E & F) With any custom bike, fender clearance shouldn't be an issue. The sticking point is on choosing tubing thickness that works for the road and also holds to some trail riding.
3) As a commuter, I'm pretty partial to road disc brakes but if rain isn't something you ride in often, I also like Campy's short-pull v-brakes, another commuter-friendly brake. Simple cantilevers would also accommodate wider tires and fenders.
It sounds like you want to start with an RST from your specifications, and customize as needed. What you really need to ask yourself is what do you want it for the most. If off road riding, credit card touring, and a comfortable smooth ride matter more than weight, power transfer, and a lively/springy feel, then the RST is a good starting point. Waterford wants to build the bike that's right for you so it's important to think of the RS and RST standard models really as just starting points on the path to your perfect bike.