I think you ned to pay particulat attention to the specific part of the code that is being applied.
The transfer switch is one area where the rules differ depending on whether the generator is used for optional, back-up, emergency, or health care purposes.
Some of these applications require an automatic transfer switch. Others will allow for a manual switch-over.
Should you use a manual switch, please keep in mind that you will be connecting/disconnecting under load, and size accordingly.