Adding an instantiated scene to the tree correctly creates a problem?

Well, it solves your problem. So… Yes!

That being said, it’s still quite a bit of extra work to solve a (seemingly) trivial problem. So if I were you, I’d still open up an issue on GitHub in the hopes of this being avoidable altogether.

The second one is (imho) easier to understand at a glance, but if you plan on using this more often, then I’d definitely go with the second option, since the parent Node3D becomes obsolete after the initialization.