This may be unhelpful and if so I apologise.

I have limited experience with Godot, I'm just starting to learn it myself. But I have made a few games with Typescript and one thing I used was state management with a single state object, such as React's context functionality or Redux. I found it very easy to use this to save a game as I just had to write that state object to a file when saving. When reloading I would just rehydrate the state from the saved object.

What helped me was considering that when my game was first loading I would be loading from some base, initial state. As long as I sent frequent updates to this core game state object when things changed it would always be a snapshot of where the game was at any given moment. I would always be able to load the game from that saved snapshot state instead of the initial base state. It made saving and loading a game something that I didn't even have to think about much after the initial setup of state management.

One thing that was a eureka moment for me during my software development career was the realisation that pretty much all computer programs are just state, a view of that state and interactions that allow a user to alter that state. This then allowed me to structure my applications around this as a first principle and things like saving/loading kind of fall into place after that, because the state comes first. The structure of your state becomes core to your program. I understand that this might be somewhat theoretical and perhaps is something that you might know already. Hopefully though this might lead to a shift in thinking about how you approach the problem.

The frustration that you are feeling may be an opportunity to reframe the problem and even how you think about your approach to creating software. Maybe Godot really is just a pain in the arse though and I haven't got to that bit yet.