If its uncomfortable it would be obvious to the dentist. I too have had problems with dental drilling. i have also raised my hand and on one occasion grabbed the dentists hand as my raised hand did not seem enough to get his attention. The discomfort was obvious. I was making audible sounds, but it made no difference and the drilling continued. This experience has left me with some big issues when fillings are needed.
You do not have to put up with pain during any dental procedure. The dentist should be able to make you numb somehow. I always ask the dentist to check the area before they do any drilling, and they have to convince me they will stop if I indicate any pain, it helps me feel less anxious.