As far as I know scripts attached to an instanced scene shouldn't be executed until the scene has entered the tree.
I'm kinda lost here. It's been like 2 years since the last time I used Godot too, some things I don't remember, some things might have changed.
I still don't get it. There's only one tree, so what are you trying to achieve here, and why can't you just create a probe scene, attach it to the main scene and do all the path finding you need?