I think the easiest way to research gen 3 flags and how they work is to use a script editor and search how the game manages the flags, since for example in emerald to re-enable the full groundon/kyogre event you'll find information at the weather station script you'll find how the game handles them for example.
I did research the flags too some time ago, in fact I should have a script (to be used as a wondercard) that re-enables all emerald legendary battles, I even made it so it will only work if you have beaten the pokemon league. The problem will be finding it, since I've moved recently and all my data stuff is mixed between computers.