You cannot bond the neutral to ground at the ATS. The neutral is bonded at the 12 kV - 480 V transformer secondary and can only be bonded at one point.
You need an equipment grounding conductor run to the 480-120/208 V transformer from the ATS to ground the transformer enclosure. Otherwise, there is no metallic return path for a 480 V ground fault at the transformer.
You are not grounding the generator neutral at the generator, so it is not a separately derived system. As such, you are correct not to switch the neutral at the ATS. An alternative would be to ground the generator neutral, making it a separately derived system and use the ATS neutral switch.
There is a possible problem with not grounding the generator neutral. If the generator is running, and there is a ground fault, the return current would have to flow through the grounding conductor to the 12.47 kV - 480 V transformer and back through the neutral to get back to the generator neutral. This path may have a high impedance and may make fault detection ineffective. If the generator and the 480 V service are close together, this may not be a problem.
Why is the fire pump not powered by the generator? If the normal service is reliable enough that an alternate source is not required, why have a generator at all?