It sounds like you are saying regardless of the Transfer switch position, the ground to neutral bond is the same bonding jumper. That is not true. The Neutral is switched, so EACH neutral has to have its own independent bond to ground. If I misunderstand you, I apologize up front.
I'm only discussing a single phase portable generator. These have a 14-30 receptacle (two phase conductors, one grounded conductor, one EGC) feeding a 14-30 receptacle. This receptacle is connected to a 14-30 power inlet box via a 14-30 cable (10 gauge for 30A). From the inlet box, the four wires go the the transfer switch.
The TS switches whatever circuits have been chosen. The conductors from the chosen circuits are routed to the TS switch. If it's an SDS, the neutral of those circuits are also routed and switched for each circuit. In the non SDS case, the neutral from the generator is passed through the TS to the SE, and bounded to the SE neutral bar, consummating the non-SDS neutral/ground bond in the SE.
In both the SDS and non-SDS configuration, the 14-30 EGC passes through the TS and is bounded to SE ground bar.
Now let's follow what happens during a source ground fault. An equipment fault in the building while the generator is powering the building. In an SDS system, the EGC fault will land on the SE ground bar. Since the neutral is switched, there is no path from the EGC to the generator neutral at the SE. So the EGC fault travels to the TS...again...the neutral is not connected here either. So the EGC fault travels back down the 14-30 EGC wire to the generator where the EGC is connected to generator ground, which is bonded to the neutral (i.e., the generator has a bounded neutral). It hops to the neutral at the generator, and clears the fault.
In a non-SDS system, the ground fault will, once again, land on the SE ground bar. But in this case, since the generator neutral is bonded to the SE neutral bar, with bonding jumper to the SE neutral bar, the EGC fault current will follow this jumper to the SE neutral bar and then ride the generator neutral back along the 14-30 cable to the generator, clearing the fault.
Now, let's see what happens when the building is energized by a non-source entity (e.g., lightning). This energy pulse is looking for ground. It's looking for a GEC and a solid GES. Whether it's an SDS or non-SDS, the energy is going to flow through the building EGC to the ground bar in the SE. It doesn't care if there is an EGC back to the generator. It doesn't care if there is a bonded neutral in the SE back to the generator. The current doesn't need or want to go there. What this pulse sees is the GEC connected to the SE ground bar, connected to the GES. The GEC and GES is ALREADY THERE! It's already connected! What more does it need?