Answer: In some cases…yes, in some cases…no, and in some cases, it depends on where you put the pillow. If it were possible to see how tight the convertible top folds when in the open position, you would see that in most cases there is very little room between the layers when the top is in the open position. Clearly a pillow would not fit in the space between the folds.
It is possible that if a pillow was put in the rear window, and then the top were opened, the pillow could damage the rear window, be it glass or plastic. It is doubtful that it would damage the convertible top mechanism or frame, because the top would simply stop retracting due the resistance from the pillow. If you were to manually force the top to retract past this point, you could damage the frame.
I have seen people put thin towels over the rear window before retracting the convertible top in an effort to safeguard the window. I’m not sure if this really helps, but it probably does not hurt. In no instance should you ever put anything inside, or under the well into which the top retracts. I’ve seen many soft objects such as a car cover cause the rear window to crack when the convertible top was retracted.