I'd love if you could send me a save state - specifically a save state, I can rename it and connect it to my existing game without disrupting my own states - of where you are in the game. Have your Fly and Dive users in the party when you save the state so I don't have to look around guessing.
However, if you'd like to do that test for me, do the following steps (and this is long, hence why I offered to just do it):
1. Go to AdvanceMap. If you don't have it, go here. Extract to a folder named, appropriately, "AdvanceMap" on your desktop. Don't put it in Program Files on Windows 7 (possibly even Vista) as it won't have write permission.
2. Load the ROM. (I recommend putting a copy in your AdvanceMap folder after you extract the files from step 1.)
3. Double-click "From Header", then "0", then "ROUTE 409 (0.30)" (below Enermy Town and above five other Routes).
4. At this point, you should see Route 409 in front of you; ignore the black-looking tiles, many tiles are a merge of two tiles which results in the nice scenery within the actual playing of the game and I'm not explaining this. Click the "Movement permissions" tab.
5. Pick one of the rocks on the left of the map (now all represented by quartets of "1" flags for non-walkable). Replace it with a quartet of "4" flags (Surf).
6. Try to leave the map by double-clicking on another map. You'll be asked if you want to save changes. Do so. REMEMBER WHICH ROCK YOU CHANGED.
7. Assuming you worked on a copy, go ahead and put it over the original ROM in the VBA folder.
8. If VBA is already running the ROM, save a state if you want to resume your progress from this point. Then reload the ROM.
9. Fly to Seanport City (if you can Dive, you can Fly; if for some reason you DON'T have Fly, check Serenity City more carefully).
10. Take the exit to Route 409. Head to the beach.
11. Remember which rock you changed the flags for? You should be able to glide over it now. Do not try to travel outside the known map here as the rocks are obviously blocking that possibility normally (and besides, the borders are unwalkable).
12. Find a Dive spot in Seanport City. Save your state (NOT the in-game save itself, and a different state that you have not yet used so you can later delete this). Take a picture where you're going to Dive (I want to see what happens).
13. Attempt to Dive. If you end up somewhere, take a picture again. Take a few more every few steps. I'll try to identify this map if you send me screenshots that I can construct a minimap with and can later tell you which map it is within AdvanceMap. When done, reload the state (I do not know if returning to the surface works or is connected here).
14. If you wish to try another Dive spot, repeat Steps 12 and 13 for each Dive spot. If any do not connect anywhere, just take a screenshot of the result and reload the state.
15. When all three are done, cease the experiment for now. I want to further see any that are connected to something for myself later. If you wish, go see what happens with the ones on Route 408, which I presume are just decorative.