I guess the main disadvantage of fitting an isolator is that the ecu loses it’s memory each time? I recall some years ago when I disconnected my battery, on restarting, the engine sounded pretty rough for the first 10 seconds or so.
I've disconnected and swapped my ecu many times and never had a problem. For the first few seconds after restarting the engine tends to idle a little fast and the sound of the ICV adjusting/optimising can be a bit disconcerting.