Correction: Once the Document layer is set to visible (tick) in the Layers Manager. it is not hidden in the PCB Canvas if the Document layer is set to hidden (no tick) in the Layers Manager.

Hi Andy when you hover the mouse on the Layers tool, do you see the scroll bar?  at the Layer Manager, when toggled to invisible, this layer's name only invisible at the Layers Tool, not hide all objects of this layer. it should be as a bug, we will fix it.

"when you hover the mouse on the Layers tool, do you see the scroll bar?" No: as in my screenshot, you can see that the right hand side is cropped so the vertical scroll bar is not visible. There does not seem to be a way to widen the toolbar window.