In RPG maker, the events are tied to the map tiles on which they're triggered. So an event that spans multiple maps would be stored on the tile that triggers it, but would contain teleport commands. So to use the Garland example, you'd have a Garland tile that when you talk to it would trigger an event that looks something like:
* Display a message: "I will knock you all down!"
* Fight Monster Party: Garland
And a Princess Sara tile that when you talk to it would trigger an event like:
* Display a message: "Thank you LIGHT WARRIORS"
* Teleport party: (Coneria Castle, xx, yy)
So while it spans multiple maps, it's stored in the tile that triggers it, regardless of where it takes the party during execution.
Conceptually, I think most events are inherently tied to the map because they're normally triggered by either stepping on a particular tile or examining/talking to it, and which tile triggers which event is important, so I can see how keeping events separate from the map might be confusing for the person making the events trying to keep track of what event index corresponds to what map tile.
However, there are certainly some events that are not tied to tiles on the map. Of particular note would be events that are triggered by using items. The "whistle" item in FF4 for example triggers the Big Chocobo menu, but you can use it anywhere; it's not linked to the map in any way. Similarly, in FF1, using the Bottle to release the Fairy seems to me like it would be awkward to try to link directly to a map.
In terms of storing the files, there could be a separate event file, but the tiles in the map can have pointers to various events. Likewise, certain items such as the bottle could have event pointers. So building the bridge would not run event 13 in Coneria.map, it would simply run event 13 from the event file.
As far as being user-friendly, I don't imagine it being too bad as long as you can launch the event editor from the map editor (or item editor or whatever other entities trigger events).
