I think there is a lot of confusion over this point ... in no small part because the code seems to be worded as poorly as possible.
First, let's keep our issues apart.
"Separately derived" simply means that the transfer switch opens / switches over the neutral. Strictly speaking, the ground network isn't part of this.
I always recommend breaking the neutral ... electricity is trying to go 'home' to where it's made, so the genny electricity has no interest in the PoCo neutral. Let's remove one source of trouble by taking the PoCo neutral out of the system.
Even though the ground and neutral are bonded at some point, it's important to remember that the ground is normally NOT carrying current. It's there like a drip pan, to 'catch' any electricity that 'leaks' out.
In the usual arrangement, you bond the ground to the PoCo neutral. Yet, with your transfer switch, you have removed the PoCo neutral from the picture. Therefore, you need to bond the ground to the genny neutral. This is usually done at the genny itself.
Now ... for the third element .... the ground rod.
Why is the ground rod there? It has nothing to do with clearing faults .... and we're not going to be using the earth itself as a conductor. The ground rod is there for lightning - that's all.
What would we call the wires from the genny to the load center? They're not branch circuits ... they're now acting as your service drop. Let's look them that way.
The PoCo has a ground rod at their tranny, and you have one at the house, even if the tranny is but a few yards away. I suggest that you duplicate this arrangement. That is, if there is any way for the genny to be seen as a 'separate structure,' then it gets a ground rod.
If the genny is actually inside the building, then you need only tie it to the buildings' grounding network. If it's 100 yards 'out back,' in a shed, it needs a rod.
Apply the same thoughts to any source of power ... be it a transformer, a wind turbine, a bank of solar panels, whatever. Keep these three (over-simplified) principles in mind:
- Electricity wants to go back where it was made;
- Ground rods are for lightning; and,
- The ground wires, etc., are not normally part of a circuit. They're for 'just in case' to make sure the breaker trips.