488 GTB windows all the way down when turn off the car

These may be two independent problems. As far as the car wash mode is concerned, are you turning off the ignition with the transmission in neutral.

 

With the car in gear switch off the ignition. Car wash mode will not be activated.


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So the window going down as you open the door is to clear the weather-stripping/door seal and then come back up, as you noted, when the door is re-closed.

I suspect there is probably a limit switch that is supposed to stop the window in its "clearance" position and this is not working so letting the window go all the way down. And in its fully lowered position there is no control algorithm to raise the window back up when the door is closed.

Does the passenger door do the same?

 

I would say that the window motor has a hall-effect sensor in it like most modern cars. The window stops may need to be relearned.

 

Put window down with button and keep button depressed for 5 seconds. Then put window all the way up and hold button for 5 seconds.