<<<< I have seen old AT's that would stay running for weeks with no battery at all and there was no trouble until you had a power failure or something, then the settings would be lost.>>>>>
The above statement is irrelevant to the question posted. The CMOS info is for boot up purposes only. ANY computer will run indefinitely with no battery if not turned off. The CMOS is not in play. The only issue here is whether the mobo voltage is mainly used for cmos retention or is it the battery only. Rechargeable batts adds another separate complicating factor. Shutting off the computer with the battery out, is not the same as taking the battery out of a booted system and putting it back in that booted system five minutes later. By your statements, nothing should be lost.
Edit: To try and further clarify: if the battery is only used for "backup" in a no juice shutdown condition, then that means the mobo voltage is the main source of charge all the time EXCEPT for shutdown.
SOMETHING has to supply voltage to the cmos at all times.
Therefore, if a computer is on, the cmos is being charged and the battery is not necessary to retain settings DURING THIS TIME. And if you put back in the battery before shutdown, it should take over as needed, nothing should change.