I think the intake runners are longer on the TR4/4a manifold, which is the one in Don's picture, and that is what makes the air filters tight against the inner fender.Longer runners are supposed to be good for mid-range power, and the straighter path compared with the earlier design is good for top-end power.
I may be wrong, but always thought the "S" was for "separate" meaning the float chamber is separate from the body of the carb.
In either event, the manifold is an alloy casting, so could easily be opened out to match larger ports if that is desired.
I would add that the pancake air filters do seem restrictive compared with stock filters, but this is just my impression, no figures to back it up. The inner fender on my TR4a had been "relieved", i.e. bashed with a hammer, by a previous owner to clear the deeper K&N filters, but now is back to standard configuration, and stock air filters.
Simon.