Welcome to the nightmare that is a shared pen based graphics.library. You really do have 65536 colours available but (for backwards compatibility) the graphics.library still uses "pens" for colours.
The palette editor only knows about those pens used by workbench for it's standard rendering and nothing of the nature of the screen itself.
On an RGB screen, changing a pen colour only affects the next use of that pen (and not any previous instances), unlike an 8-bit screen, where pen management is much more important.
