Would you have room in the messenger bag the 2-3 days you do ride with the bag to fit in extra food? Perhaps you can store non-perishable items like drinks, snacks, etc. where you work and then on the days you do not have the messenger bag, all you'd have to bring in is anything perishable in the "tupperware". Would that work?

On the days you do not take the train, you will hopefully have food caches at work so you wouldn't need to carry alot of stuff.

As far as containers, I can't help you there although you probably should use rubber bands no matter what container you use just to be safe. Hate to see last night's spaghetti sauce running down the back of your jersey while riding down the road

Jay