1. There is the vanilla application, though. As far as I know file names should have no effect on what the executables do and I have seen other mods that did not overwrite vanilla Terraria.1. This is necessary for the game to work, as it isn't just the mod on it's own, it's the mod + Terraria.
2. STW automatically saves it's files in a separate folder - not sure what you're talking about here.
3. This is due to the fact that STW is currently in it's SP beta - when it becomes an MMO this will no longer be an issue.
2. The installer has an option for where the saves are. If you do change it, it appears to break the game, you cannot get ingame anymore until you reinstall.
3. I assume I will have to manually delete the world to make it playable again? And by MMO do you mean MMO or simply multiplayer capability, because I don't quite see what you are envisioning, is there a post on that?
4. Will persistent maps be a thing?