It's true the mod system for godot is flaky. Trail and error will lead to more experience for the best way to mod files (that's how I made my mod).
1. var {} is a dictionary, and it's true, you can't just overwrite it. You have to modify it after the object gets created. Alternatively, you can overwrite the whole function or class where the var is being defined.
2. <addto -1> should add it to the beginning, but actually overwrites the whole function or class a lot of the time. <addto x> will add it to line x. I use addto x most of the time, and it seems to work well enough.
3. I don't use a compiler / code editor, just notepad++. When I break the mod loader, then I have to extract a fresh version of strive, and overwrite all files. It's a pain in the ass, but it's what I know.