Are you guys using a station exhaust system of any kind? A roof exit exhaust does make it more difficult to connect the tubing cuff by the troops, but it has been done before in other industries. Just think about the extra space needed for exhaust pipe, shielding and insulation and the extra heat in the body and compartments you might have and lose as well unless you run it outside the body. City buses are using top exit exhaust in many areas but the exhaust does exit to the rear of the passenger compartment area in the engine bay with insulation to reduce heat.
Top exit exhaust helps to greatly reduce the fireground emissions, but at what expense and cost in the big picture? Check with the manufacturers and get some referrals and their opinions before you lay out the specs. They might have other options for you to consider. Good luck, bro.