The generator is not bonded (Honda) but even if it was, the worst thing I can see is you would have some neutral current on the ground. Which wire would burn up?
I have seen plenty of improperly wired SDS transfer switches and no outward problems. As a practical thing it is the same as those 4 wire sub panels with a rebonded neutral.
If your generator has outlets on it, the neutral is bonded to the generator frame. Nearly every small generator in the US is designed like this. Permanantly mounted generators can remove this bond, but it's generally not feasible to remove this bond on portable generators as it would float the neutral in the gen when running stand-alone. Leaving the only proper solution as switching the neutral in the transfer switch.