Dean pretty much summed it up, and he's probably the best to ask. You aren't going to find many folks who can really answer the question, as there are not too many RCR40s really shaken down, and there are even fewer SLCs. Dean has one of those 40s, and has driven one of those SLCs.
But just look at the facts:
The SLC is longer, with a longer wheelbase, bigger cabin, central fuel tank, and cabin that fits a standard seat. The cage is integrated into the design.
For "practicality", the doors open up and forward, so you can get out of the car in a parking space. The cooling tubes do not run through the center of the cabin. There is a real center console, and a real steering column.
The SLC body is a modern design and makes downforce. The engine compartment is bigger and can use almost any transaxle/engine combo you want. The rear suspension has inboard shocks, and the geometry was fresh design all around.
The SLC is also lighter.
So, it's lighter, easier to make more powerful, faster, more stable, safer, larger, and more practical.
I bet cost to build is going to be similar. For me, using the same drivetrain would have been much easier in the SLC.
So why even think of a GT40? Styling is one. Sound may be another (180 headers). And I am betting the 40 will have a more go-kart feel, with more sensation of speed. Since I am not building the car as a race car or track weapon, I just want it to be fun. And fun is measured in difference ways than speed. The styling, sound, and the ultra-low driving position were higher on my list.
If you are building a track car, you should definitely build an SLC. If you want an exotic car with pace to back the looks, again, SLC. In fact, I would say if you are asking the question, you should go SLC. The reason to build a GT40 is if only a GT40 will do.