I have encountered a 40-minute connection time with the same warning. Unless it is a mechanical issue, I would say you are on the hook as AA is not going to be responsible for weather, air traffic delays, etc. IF your flight leaves BOS on time and with just carry-on you should be Ok but one little hiccup getting out of BOS or a delay in landing and it could be problems.

I just flew on AA and started out with the 40-minute connection. They then changed flight times on both flights and I ended up with 2+ hours. It seems the airlines have continued to build in a lot of "fluff" into their flight times. I would have been fine with the 40-minute connection as we departed DAY about 30 minutes late (de-icing) but with the short flight time, we still arrived CLT a little early.