MVVS does not prohibit stopping the engine with the choke. They just warn that opening the throttle with the choke on may damage the reeds. They are fragile.

There is no risk of flooding the engine into hydro lock. The largest load of crap I ever heard.
The jets are so small, that such a thing will never happen in the time needed to stop the engine, which by the way still is pumping and expelling gasses at the same time. It's the nature of the two stroke beast.
I find the engine easier to start if I used flooding to stop, or choke the engine well without the ignition on before I store the plane. At idle, the engine is slightly oil starved. The choking brings in extra fresh oil that conserves the engine. The extra gasoline carries the thinned oil in all nooks and crannies inside the engine by aerosol mist, and capillary action.