MMF2 gives you as you had mentioned access to new extensions and Alpha channels, but their is also a ton of other differences. Check them out here...
As far as Flags go think of them as switches, flags can either be on or off, True or False. So prehaps you want to pick a object randomly and test for to see if the flag is off, once that condition is meet in your actions you turn the flag on, so the action is performed again, things like that are where Flags can be useful.
Behaviors are identical to the main event editor accept your events are capsulized inside the object, this events of course run at the end of the main loop as the main event editor events run first, Cool for compartmentalizing your code, but can also end up slowing up a game.