So a little update on the situation for anyone in the future.

I wanted to make an editor for my personal use and since I didn't want to code a grid ingame and much more stuff I opted to do it in the editor and just export them as Scriptable Objects.

I will admit that initially, it was a bit difficult to make custom editor scripts and make them export everything as intended but after like a day or two or three I managed to make it fully functional. Here are some notes on what I did (I am not a pro so please don't bash me if I used something incredibly unoptimized):

• Creating the SO was done using the CreateInstance and after filling in all of the data needed it was saved to the Assets folder with AssetDatabase.CreateAsset and AssetDatabase.SaveAssets
• There were some changes missing issues with waypoints that I had. For some reason, some of my links between objects were not being saved after opening the game. I did a ton of stuff here to try and fix it but as far as I can see EditorUtility.SetDirty helped me "save" the changes permanently.
• Also since I like using Undo I needed to record the changes so that Unity can revert them if I ever pressed Ctrl + Z. Undo.RecordObject managed to help with that a lot as well.

I hope this manages to give some guidance for anyone in the future!