Hi, Erin. You have pretty much answered yourown questions. You will have to work with your professional on the natural breaks and how much to do. Your pro will pretty much demand that he use water based since he can put on a couple of coats in a day and it would be a week of back and forth trips for him with oil based.
As far as an allergic reaction to water based, there are people who prove to be allergic to about anything. I think that you will find that the number of people who are allergic to water based is pretty darned small.
There are commercial finishes that out perform oil or water based poly. They have to be applied in strictly controlled conditions by spraying. The conditions in your house--or any house-- will not meet the criteria so this is not a viable option.