I just rebooted and found myself in spam hell. All the applications were ones I use, either when gaming or editing code. A window popped up covering the field where I was expected to enter a password. Worse it was not possible to move or minimize that window. I had to fill in the field and make it unusable.
This may not be completely solvable in Thunderbird, but a list of other applications that could be brought to the front would be a lifesaver. It could be just another pop-up, but it could wait 10 seconds before appearing. Probably near the bottom left corner to avoid becoming part of the problem.