I don't know much about C# with Godot, nor do I about VS Code. I think Intellisense is code completion, and although it's not full code completion, I get all of my needs served by using Atom with the necessary files open in background tabs. My personal philosophy is that I shouldn't be getting too used to little assistants like this until I have professional experience, however I don't know your experience level.
If you're interested in editing the Godot source, I would say to just start reading through the source, making sense of it and when you think you've found the reason why you can't use Intellisense within an #ifTOOLS block (it sounds like you've researched your problem and may have a starting point to begin editing), start playing with it until your problem is solved. Again, I don't know your programming experience (probably more than me), but Godot is an open source project, you're meant to hack around with it and learn. You have nothing to lose aside from the time spent messing around in the code, but if you're developing games on a hobbyist level, you probably have enough free time. Go for it. I'd be interested in seeing your edits, just as an idea of where I might want to start myself.
https://github.com/godotengine/godot/tree/master/editor/plugins
I wish i had the insight necessary to help you here, beyond the abstract ideas.