When your framework is made to build apps that may be downloaded over the air on the nation's least reliable cellular network, you should at least try not to include the kitchen sink with every app. Waiting for the app to download is the user's first impression after clicking "buy".
Hello World is not just an edge case - it's a lower bound. There are plenty of non-trivial apps that can be implemented in under the ~3MB overhead for Flash. Once multitasking arrives, this kind of overhead will be even more important, because small single-purpose utilities will be more useful. Also, if the overhead is 3MB on-disk, the in-memory overhead is likely to be even bigger, and it's not likely that it could be shared between several Flash utilities running simultaneously.