I think that the chicken and the egg might be confused here.
A "Separately Derived System" is a premises wiring system that has no direct electrical connection, including a solidly connected grounded circuit conductor, to supply conductors originating in another system. (summarized from the definition in article 100).
A separately derived system has to derive its power from some source; this source could be the secondary of an isolating transformer, the output coils of a generator, a battery with an inverter, etc. The point is that there is no 'galvanic connection' between the power source and anything else. There is no need for the utility to be present at all. You could have two generators and set things up such that each is a separately derived source relative to the other.
The wiring between multiple sources determines if they power separately derived systems or are both part of the same system.
If you have two sources with neutrals tied together, then you do not have separately derived systems. You simply have _one_ system that happens to have two power sources.
If you have two sources, but their neutrals are not in any way tied together, then you have two separate systems.
The question about SDS and transfer switches may be understood from the general requirement that each solidly grounded system have one, and only one, bond between neutral and ground. Once you have combined two sources with a transfer switch, you have created a single unified system. This system must have only one neutral-ground bond.
If you have ground-neutral bonds at both sources feeding the transfer switch, then you much switch the grounded conductor, so that only one ground-neutral bond is present in the system at any one time. If you have a transfer switch that doesn't transfer the neutral, then one of the sources must not have a neutral-ground bond, and you must depend upon the neutral-ground bond at the other source.
As Smart$ points out, it is often a design decision; you can generally tie or lift the ground-neutral bond at the generator, as suits the application and the particular transfer switch used.
As iwire points out, the particular design choice is often set by ground fault protection; if there is GFP then it _may_ force the location of the ground-neutral bond to be at the source in use. Note that I think that it would be possible to design GFP that would work with non separately derived systems.
-Jon