Is it bad practice to use all of the different Control nodes (NinePatchRect, TextureButton, SpinBox, etc.) without adding them to a Control or Container node so that I can just position them manually without any influence of the parent container?

I mean, you can do whatever you want if it works. However, using Control layout is very powerful once you figure it out. Especially for user interface, which you want if you scale to different resolutions or aspect ratios. It's a nightmare to try to do that manually.

    cybereality Especially for user interface, which you want if you scale to different resolutions or aspect ratios.

    Also known as responsive design.