They have a no eating/drinking rule. That said, they do allow cups with lids, bottles, juice boxes, etc. I've seen drivers turn people away who had ice cream, cups with no lids, popcorn, a can of Cheese Wiz and sleeve of crackers, and other food. I've also seen them let people on with bakery bags obviously containing food, but often reminding the person of the no eating on the bus rule.
I think a lot depends on the driver, and how many people are going to be expected. This past August I walked onto a bus at around 1:30 at the AK, headed to the BW. I was the only passenger on the entire ride. I am pretty sure that if I had food, it wouldn't have been an issue. But IMHO it's very rude to carry on food on those crowded early morning and late evening busses. It's often standing room only, and too easy to spill food onto a fellow guest. I've actually seen it happen, a lady was handing out pop tarts and juice boxes one morning a few years back to her kids. The bus hit a bump, the kid squeezed the box, and sent a stream of juice flying out of the straw and down the back of the person in front of them. Not a good way to start the day...for anyone. The wet passenger, the overwhelmed mother, and the fellow passengers who then had to listen to the shouting match that began. Oy!
Considering it takes a total of five minutes to eat a muffin and juice, why not just get up five minutes earlier and have your meal at the resort before you leave. It's a lot easier on you and your fellow guests.
One more note--sounds like you've got commando style touring planned. You might want to slow down a little, it's easier on the stomache and the nerves, and you'll have a much more enjoyable time
Anne