Don't make more of this than it is.
The transfer switch is probably arranged to make your installation nearly mistake proof. That is, it will have sets of lugs, grouped together and clearly identified as to main power, generator power, and load. From that point on, it's just "connect the dots."
Likewise, the generator likely has a big ground lug for you to use.
As for the "parallel path" issue ... at this size there ought to be no doubt about breaking the neutral, and having a separately derived system. When the generator is running, there is no reason to remain connected to the PoCo wiring in any manner.
