I agree the genset can fail. But honestly I consider the risk of the genset frying everything very slim vs. a surge coming form the pedestal.I want the protection as close the pedestal as possible.
Maybe I may fry my 50 amp cord if a large surge strikes However everything after the EMS 50 should be protected.
If surge is installed after the transfer switch than the transfer switch itself could fry along with more internal wiring if the pedestal produces the surge.
I'll take my chances with the genset and focus protection to issues coming from the pedestal.