Very few if any of these charging systems keep up to the load when idling at a traffic light, they discharge, sometimes quite heavily. They are not like modern automotive charging systems which put out all kinds of power even at idle. The charging systems on these bikes need more rpm to bring the voltage up and start to charge.
So when you are sitting at night in heavy traffic, headlights on, possibly point/coil high draw ignition, inching ahead, blipping the throttle as you notice the lights are getting progressively dimmer, the thing you really need is a great big old lead acid battery that has a ton of capacity and will still function below 12 volts, nevermind 13.
What happens to the Li battery in this scenario is, lights out, limp or protection mode for battery(5.4 volts), engine dead, call Triple A.
Been there and so have a few others.
You are correct, after trying them on two older machines, I know these batteries are not a good fit for our older bikes with their relatively low output charging systems.
If you were to do a poll of all the Commando owners here asking how many had batteries with resting voltages above and below 12.86, you will find a landslide on the below 12.86 side.
That, and the info from Shorai on minimum voltage requirement, tells you all you really need to know.
Glen