So far, the world map design matches up pretty well with the layout on the ground, though the western areas and the immediate vicinity of the Water Temple are a bit wonky. Come to think of it, given its placement, is the lighthouse affiliated with Pandora? The game text gives no hints either way.

(Pandora is used in the video linked above as an example to show that it doesn't matter where within a cell you land; the whole thing goes to the same place.)

Only Matango, the Sprite Village, and the cannons have landable tiles, so it's interesting that so many other cells have landing targets defined, even if the middle row of the western half seems to be overdoing it a bit. The seasons even match up with their arrangement on the ground, regardless of the trees all looking the same from the air. The winter target (for cannon travel) is the only one that matters, however, even though the summer zone is the only one not given a landing zone. Also, the Sprite Village and Wind Temple seem oddly displaced to the west, and the Moogle Village isn't represented at all.

(The Great Forest landing spots are demonstrated in the video linked above.)

* As noted in the story section, landing here after the Sandship events warps the party to the screen south of Kakkara immediately upon arrival.

Other than the weird pocket dimension the Sandship seems to exist inside of, the desert layout matches up pretty well with the map. Also other than the weird Sandship pocket dimension, the desert seems a lot smaller on the ground than it looks on the map. Yes, many parts of the Gaia Lowland region also have a one-to-one relationship between field screens and world map cells, but most Gaia Lowland field screens are significantly larger and more interesting.

(The Sandship landing spot is demonstrated in the video linked above, both with and without the event flags set.)

It's remarkable just how much nothing there is on this continent, even before taking into about the repetitive geography on the ground. Multiple landing zones go to different points on the same maps, an interesting bit of attention to detail, even if the maps aren't really large enough to justify it.

More curious is the cell on the western edge of the continent that duplicates the landing zone for the Icy Sea Lion Village. It's not even unused data; just enough of the little island in the bay and the peninsula to its north poke into this cell that it's possible to land on the western tip of either and end up in the village, which is supposed to be far away to the northeast! It would make more sense for it to duplicate the resort landing zone, but perhaps the mappers didn't realize there were any landable tiles in the cell.

Speaking of the resort, it's always bugged me that it still shows up in green after rescuing Salamander. There are other places where the world map updates itself in response to story events, so why not here? And the area is frozen over for so much of the game, including the entire time you can fly freely, that it feels like it would make more sense to just have it show up as icy in the first place if it's not going to change. That green patch in the southeast doesn't correspond to anything on the ground, either, for that matter. And, come to think of it, there's also no sign of Santa's house.

The Nikita landing spot is noteworthy mainly because it's involved in a glitch that allows for farming extra sword powerups.

(Both Icy Sea Lion Village landing spots are demonstrated in the video linked above.)

That's a huge number of cells that all use exactly the same landing point in Northtown, and most of them don't even have any landable tiles to begin with. I get the impression that they originally went to a variety of different locations before the content was stripped down, and then were all changed to Northtown (except the one cell that duplicates the ruins landing point instead) as a "just in case" measure.

The other big mystery about Northtown on the world map is what that animated circular thing in the southeast corner of town is supposed to be. A carosel? A racetrack? A playground? A particularly fancy fountain? Whatever it's meant to be, there's nothing that corresponds to it on the ground.

(The video linked above demonstrates landing on the eastern edge of the continent and ending up in Northtown.)

Most of the mountain is just a bunch of nothing, and there aren't even any landable tiles for the summit path destination, which would let you skip most of the climb if it were usable. I think all that helps support the theory that you weren't originally going to have flying here as an option on your first several visits.

(The normally-unusable landing spot near the summit is demonstrated in the video linked above.)

I suppose this is to be expected. You wouldn't expect there to be anything else here, and there isn't.

The triplicated landing zone, even though there aren't any landable tiles beyond the castle itself, is another sign that there was more planned for this region.

The entire continent becomes landable during a certain late-game event, so all nine cells are meaningful.

Note that the landing location is the same place regardless of the current stage of the game, even though there are two significantly different versions of the location depending on whether or not the sunken continent is surfaced. Most areas of the game that have alternate versions, such as the Water Temple when it has monsters inside, use a separate copy of the map. Not so here. Landing data never changes, so that forces the game to use the same map for the Wood Temple exterior throughout. The differences are accomplished through a more dramatic and extensive application of the on-the-fly map modification functionality more typically used for smaller changes, like opening doors or deploying bridges.

* This Mana Fortress landing zone doesn't work properly. Its arrival coordinates aren't aligned correctly to drop the party off in a valid location, resulting in Flammie flying right past the fortress and dropping them off in empty space beyond it. However, the very presence of a landing zone for it here suggests that there may have been plans for an alternate way to reach the fortress, perhaps by way of an unused cannon travel route, or perhaps by simply having the fortress itself at a fixed location within this cell. The fact that calling Flammie from the fortress always takes you to this area (though the exact spot where you lift off is further west, due south of the lighter spot on the southeast corner of the coral reef) may make the second option more likely. Other the other hand, maybe it's just here for testing purposes and was set up for an earlier version of the fortress design.

(The unused Mana Fortress landing spot is demonstrated in the video linked above, both before and after the game allows entry. The Wood Temple landing spot is also demonstrated, along with a brief explanation that both versions of the location use the same map.)

As with the Wood Temple landing zones, the Mana Holyland landing zone goes to the same coordinates on the same map regardless of the stage of the game, even though it looks like a completely different location after clearing the area. The game dynamically alters the map itself so thoroughly that it's entirely unrecognizable as the same place. (Note that this applies only to the initial screen you reach immediately upon landing; the rest of the forest uses separate, far more conventional maps, and you're simply unable to reach them anymore after clearing the area.)

* Mop's Secret of Mana Editor lists the south central cell here as "Reserved for floating manafort." Trying to land here, assuming the game has been modified to allow that, has the same effect as making a landing on the Mana Fortress normally. The game presumably uses it internally for that purpose.

The Mana Holyland cell has no landable tiles until after a certain late-game story event, which alters the cloudy tiles in the middle.

(The Mana Fortress landing spot is demonstrated in the video linked above, both before and after the game allows entry. The Mana Holyland landing spot is also demonstrated, along with a brief explanation that both versions of the location use the same map despite apparently having nothing in common.)