UPDATE 2018/03/07: Thanks to a conversation with Noisecross, I was able to fix these bugs in a more professional way. Therefore, I released this new version.
Hello everybody,
as a compensation for being helped a lot here, I decided to share a simple ips patch I made by using solely FF5e Map Editor.
That means anybody could have made this fix (but I didn't see anyone made it so far, so here you go^^). Actually I wanted to fix the bugs by changing Background1 of the tiles, but then I found out that world map tiles only have Bg0. But I found alternative approaches.
What exactly is fixed?
Ghido's Cave Bug: When you (accidently) land the Airship or Hiryuu on Ghido's cave in world 3, you can never embark them anymore because there is no way to walk on this tile without entering the cave.
How I fixed it: I exchanged the cave-entrance-tile with another one which looks the same, but has different properties (this tile is used for Jacol cave and Pirate's cave afaik). So you can't land Airship or Hiryuu on this tile anymore. But you also cannot enter the cave while riding Boco (but seriously, that feature was unneccessary anyway^^).
How I fixed it now: I changed 3 bits in the properties of said tile, disabling the landing for Airship and Hiryuu. Additionally, I disabled the Hiryuu's ability to fly over this tile (kinda unneccessary, but since it also can't fly over the over cave tile, I decided to go for it for the sake of consistancy.
Chocobo Elder Tree Bug: While landing the black chocobo or Boco on one of the two entrance tiles of the tree in world 3 is not a problem because the presence of the chocobo "blocks" the entrance, landing on one of the other 7 tiles can be a serious problem. If you do that, your chocobo is lost forever the moment you enter the elder tree.
How I fixed it: I made the inside of the elder tree accessable on the world map as long as you enter from the right side (Library side), so Merugene/Melusine battle can't be missed. The only downside is that the short scene where Butz, Krile and Faris talk about losses easier to miss. But that was missable on vanilla anyway by just not approaching the trunk.
How I fixed it now: I changed 9 unused tiles into copies of the 9 forest tiles, with the exception of disabling the landing for the black chocobo. Then I replaced the 9 tiles of the Elder Tree with new 9 tiles. So Black Chocoboes can't be lost anymore. What about Boko? Don't worry, I thought of him too. On one of the 9 new forest tiles ("right/western edge of forest"), I disabled the ability to walk for Yellow Chocoboes. (You can't take Boko to the Desert/Pyramid anymore, but in exchange, you can't lose him)
Credits to noisecross for building and releasing FF5e Map Editor as well as encouraging me to work further on this patch.
The ips must be applied over an unheadered ROM. (it works with any version afaik)
We have EVEN MORE themes now, but some old ones are gone...