For tax purposes, your roommate benefits from using large amounts of space, since the rent for the space she uses exclusively for the business is tax deductible. There may be a deal here, where she pays 2/3 of the rent and utilities and you get paid to put up with the business. She then writes off like 40% of the rent, generating something like 8% off the sticker price of the home.
If she has employees or customers coming by, your city might object based on your housing lot’s zoning. Although, it doesn’t sound like it has grown to that big of a problem yet. (I guess you can tell yourself it could always be worse, if that provides any comfort).
You may want to talk to your landlord about the line in the lease. However, my understanding is that landlords typically include that line in their lease to satisfy zoning requirements, and probably won’t want to get involved.