With the the exception of the few ONR-owned stations that will be used, the third-party owned former stations might have indoor areas that used to be waiting areas but are now either vacant or repurposed. Some buildings are publicly-owned, some, like Huntsville, are private. Gravenhurst is obviously habitable; I'm not sure all are. Regardless, none of the tenants are public entities that I am aware of.
As far as I am aware, ticket sales are online/kiosk or on board with the exception of the staffed stations and PBX flag stops. The ONR would have to negotiate with each individual tenant, vet their employees then train them on their systems. They got away from ticket agents in small towns for this reason. This would also be compounded by the scheduled stop times. Some are within normal business hours; others are not.
Cost and liability. ONR would have to rent the space, isolate it from other areas of the building, heat it, illuminate it, monitor it, insure it, then probably wait until somebody calls it home and burns it down (how the wooden kiosk at Washago hasn't burned down yet is beyond me). There is also a matter of passenger safety. True that they have to power, monitor and insure the kiosks but they don't strike me as very flammable and aren't attached to a century old structure.