I've only seen original applications use clear silicon on 69/70 in the side scoop and a few end caps to body joints, but the current belief is that both received sealant. The end cap sealant started in 67 at the LA plant and was continued at AO Smith. The clear is often difficult to see and with time appears to shrink and the end caps have a very thin edge to hold it in place so not sure how well it stayed in place.
Finding examples of the side scoop sealant is allot easier than the end caps
The taillight panel and the front fenders were sealed using a very dark grey or black seam sealer to seal them to the body.
Not sure what you mean by black out. If your referring to the application of sound deadener in the front wheelwells that was not a factory practice on 68-70 Shelby's. Though many dealers surely talked new owners into paying some extra dollars to slap some on the cars when new to protect them from the elements in many parts of the country. I would expect to see the pinkish backside of the injected "plastic" with areas of black bonding agent (to attach brackets and such) as well as body color overspray on the back side of the fender. On the inner fenders I would expect to see a combination of (front to black) engine compartment black or at least overspray, red oxide primer and then body color at the rear. All over some sealers at the proper panel joints.