The message comes up any time there is a unexpected change, voltage drop, voltage peak, unresponsive, etc, etc, etc, with the retractable roof, or, the rear gate window. There is no bypass, edit: with one exception.
Exception Edit: Sometimes the TGM will forget the closed and open position reading for the tailgate window. This will throw up the message, but with the tailgate closed, you just use your key in the tailgate and roll it up. It will roll up a few inchs at a time, and stop. You repeat the process until its up all the way. Once all the way up, you hold the key for 30 seconds, and it remembers the up position. Then you repeat the process for down, and its learned. However, this does not help you with your current situation.
You may try a reset to the TGM (tailgate module), by unplugging it, and plugging it back in after 10ish minutes, but i doubt it will do anything. The TGM is located under the plastic cover of the tailgate.
Check over on youtube, channel WatchJRGo. He rebuilt almost the entire roof/tailgate system with great success, he collaborated with me a bit on his XUV and Aztek.
The only question I have, when you use the key in the tailgate, can you hear any actuators engaging/disengaging? On mine, I can hear them when the go into motion, even if they are at the end of their motion, I can still hear them try, before the TGM disengages them.
Ultimately if it isnt solved with these simple methods, a Tech2 might be your only way to get the specific issue that is the problem.