I'm not sure how you could avoid putting your face down the hole. Only thing I can think of is to cover the hole with a towel and twist your neck to the side. Sounds uncomfortable for the duration of the massage.
How about - their cushion over the hole, your towel over the cushion. Lie further up the table so you're not suffocating in the cushion.
If you take gel, you can always make sure you clean your hands after you leave.
The mask is the problem if they don't wear one. Also the lack of air movement in the small room if they don't have windows. I mean, what about your clothes.
You could go mad trying to think of ways to reduce your risk.