I think the "mystery flags" in ff4kster to which you're referring might not be event flags. They might just be other bytes or bits of RAM that toggle on or off depending on the situation.
Regardless, I can think of a potential issue cropping up with this plan: there are some non-event related things (which, as yet, can't be edited with ff4kster) that depend on event flags: the Overworld Terraforming (Agart crater, mist mountains, broken damcyan), the ability of the Enterprise to take off, the ability of the Enterprise to go to Zot, "mystic silver," Magnetic Magnes Cave (you can change whether or not it's magnetic, but not which flag controls the property), the Enterprise crane, the Falcon drill... There may be more, but that's all I can remember at the moment. All of those things are affected by event flags, and FF4kster does not allow you to edit which of those flags affect them. I also don't believe FF4kster documents which flags affect them by default. The information for many of them is on these boards, but not all in one place, and not necessarily all of them.
That's the most info I can give you right now about it,
What you are trying to do isn't necessarily impossible, it might just be more work than you thought initially.