That’s a very valid concern, but nope! The window auto stops for me when going all the way up and down. The window timing shouldn’t be a problem because, from my best guess, the window regulator is designed to work independently of the main body ECU. There are two reasons why I believe this:
1. The window regulator doesn’t care about the position of the window. In most automotive window regulator designs, the motor knows when to stop by tripping its own circuit breaker. The circuit breaker is tripped if the motor tries to draw more power, which will only happen if the window is blocked. We can see this behavior even when operating any of the car’s windows in the fully closed position. You’ll hear the window regulator try to move the motor for a short moment, and then stop.
2. The only other control wire into the window regulator is MXP2->LIN and it most likely isn’t used for window position data for normal up/down operations. LIN is a very stripped down version of the CAN BUS which allows for bidirectional data transfer over a single wire. This did have me worried for a second because there is a possibility that this could be sending data back to the Door ECU for window position/stop position to tell it to stop the motor. However, if it was really the case that the window regulator didn’t know how to stop unless it sent a signal back to the door ECU, there wouldn’t be the AUT2->AUT wire for the auto window functionality and we wouldn’t observe the behavior in 1). My best guess is that LIN is used for controlling the window regulator for special functions, such as “all windows rolling down” with remote long press. As to why Toyota didn’t just get rid of the individual wires for up/down/auto window control and just use LIN, I’m guessing it’s for reliability reasons.