Perhaps someone more knowledgeable can weigh in-- I'm just speculating from a lay perspective. The bottle configuration likely means less states are available due to the confines of the system, and these states are higher energy. I'm thinking something like the Casimir effect, where the boundaries of the system impose conditions that limit the total number of states. Could this explain the discrepancy? Something that could potentially corroborate this idea is comparing those boundary conditions. Do neutrons in larger "bottles" decay slower, and neutrons in smaller "bottles" decay into protons even faster?
I have been fascinated by neutrons for quite some time. I'd not heard of neutron bottles before. Researching about how ultra cold neutrons are trapped was quite interesting, as I had not thought it possible that they could be held in any sort of container.