Best to be forgiven than to ask permission. I snuck my dog on a train once. The ticket agent in the station said they would stop the train and put me off if I was caught. I had just finished hiking over 2000 miles on the Appalachian Trail so I wasn't afraid of a little walk. Didn't get caught.
I snuck a cockatiel on a bus from Veracruz to Catemaco, 4 hours. Didn't get caught.
Usually the dog is put in the sleeping berth below, not in luggage compartment. If the trip has two drivers that would be a problem. Visit the bus station and ask to see the sleeping berth and how many drivers are on the trip. At least you could walk the dog on breaks.