This is definitely an issue for many VR developers, and I think is an issue with game engines in general.
XR tools and similar toolkits offer you a shortcut by providing loads of functionality out of the box so you can hit the ground running, but it also means that you're skipping over the fundamentals. Especially if you're new to Godot you're not only skipping over the fundamentals of XR development, you are also skipping over the fundamentals of building games in Godot.
As more and more developers choose Godot and get experience with this, and as a result more and more information is made available through blogs, devlogs and tutorial videos, this becomes less and less of an issue, but right now it is easy to get on the wrong foot with things.
Godot itself has a few quirks that don't help either, for instance Godot 4.0 introduced the ability for you to add nodes with a script attached automatically through the `add node` button, but most of XR Tools scripts are design to work in conjunction with a scene and you need to use the `add child scene` button or things won't work properly.