Hi Kent,
I have come across this before, and I do believe there is a timeout to kill the Transmitter when there is no activity while in command mode, just not as short as the timeout timer. Not sure what it is set to, but you should be able to search the source file and see. From my experience, the Timeout Timer is looking at the Receiver activity and not the Transmitter activity, and does still operate while in command mode.
My situation was someone put a repeater in command mode while traveling and went out of range of the repeater and could not take out of command mode. I brought up the repeater later and it was not keyed, but as soon as I keyed the repeater it gave the command telemetry and stayed keyed, so I took it out of command mode. Hope this helps.