mrcoffeect,
While you may technically be right about whether or not food is intended to be hung in the shelters, common practice of the VAST majority of the users is that it is. It is also a pretty hard and fast, unwritten rule that you do not mess with another person's gear unless you have specific permission to do so, or they are your very trusted hiking partner.
The two statements above are FACT as it exists on the AT. If you have a problem accepting those facts, I strongly suggest that you choose to camp away from the shelters. When living within a group, YOU need to conform to what is the norm, not the other way around. If you cannot, or will not, then it is on YOU who needs to alter your plans.
My position is that I'm good either way. If the majority prefer or agree to hang food out, away from the shelter, than fine, I will too. If most folks are comfortable hanging it in the shelter, than that is fine by me. I've never, ever heard of a bear causing anyone any harm by coming into a shelter for the food. Tents, yeah a few times.
When you choose to place yourself in the position of living closely with others, flexibility is the rule.