Hello,
yes - i understand what you mean now. But this is actually intended.
The map is just a world file, it does not include the configuration, the configuration is global for the server with which the world is being run. You can change these settings at any time in the /steamapps/Eco/Eco_Data/Server/configs directory. Difficulty can be found in the Difficulty.eco. Meteor Time you can find in Disasters.eco.
The reason for that is that singleplayer pretty much is a server and on servers you only host one world at any given time, otherwise you need a second config directory. Implementing the settings into the savegame might be something to think about, but it would be hard to do it in a way so only singleplayer is affected, as admins might want to change stuff on their servers while the game is running in the old school way.
If you want to play with one of the earlier settings on a different map, you can ever change the configs before booting the server, changes can be made at any time.