Sure, in those rare cases when the transmission has to drop two or more gears, there will be some additional stress on the synchros, but in general driving it should not even be a worry.
Just like most people don't downshift at high RPM during normal driving conditions.
I agree with you that with these automated manual transmissions the driver has no control with how the transmission shifts, so you have to trust the engineering behind it.
Personally, having experienced their operation, my biggest worry is clutch wear, as these transmissions slip the clutch a lot during slow speed maneuvers. I guess one would have to adjust their driving style to minimize that slippage as was suggested in this thread.
Most people however don't even know how to drive a manual transmission so how would they know when the clutches are slipping excessively?