That's a max speed, not an average.

And again, for this fantastical train, we're earning the privilege of doing in 12 hours what a plane will do in 6.

Does that six hours include travel to the airport, check-in, security clearance, boarding, deplaning, baggage collection, and travel from the destination airport back into the city?

If you factor in all this extra stuff, it looks more like 9-10 hours.

You have most of that with a train too, other than the security clearance (for now). But assuming high-speed train travel became something more than the sideshow operation that is Amtrak today, security screening of passengers would very likely be implemented.

No you don't. As someone who lives in a country with functioning high speed rail and who uses it regularly, let me tell you how it works here:

You go to the train station, which is in the city centre. You use a subway, tram or bicycle to get there. You walk in, go to your platform and enter the train. You place your luggage in the luggage rack and take your seat. When the train arrives at your destination or interchange point, you grab your stuff and leave. Sometime in between, staff will walk the train and check your ticket.

No long transit to/from the station. No check-in, no security screening, no baggage drop-off/pickup. It's a train, not rocket science.