Don't recall having this issue on our '03 CRV, nor on my '99 Camry, nor on my '10 Tundra (my '11 Camry was a manual so it doesn't count). Not sure on my '21 Corolla though, haven't needed to remove the battery, yet. Only issue I've seen on the '03 CRV is that the auto up/down on the driver's window forgets and has to relearn.
Maybe all my vehicles have been older? Maybe Toyota is really behind the times...
I *did* have a problem with the throttle body on the '11 Camry, I cleaned that and the darn thing forgot how to idle. No idea why, it only has one job in life. When I cleaned the throttle body on my '10 Tundra, it simply ran better.