Thanks Xerra.
Yes, some things can be avoided by doing a bit of research beforehand. The Godot scene tree concept does introduce some unique challenges that I've never experienced before because I never used such a system to keep track of game objects. The issues seem to slowly creep up on you as the size of the game grows.
Choices made in the scene tree structure can really impact you. I'm getting better at it and I'm just going along with it. Sure, it takes a bit more time to make progress, but that's fine by me.