Moving/resizing the application window is a bit of a faff about.
The floating windows stay in place and draw on top so can obscure placement, resizing and it’s hard to grab application titlebar or window edge when it’s hidden below them.
And then the floating windows need be repositioned. Arrange windows is easy, but it loses any custom layout.
If the floating windows were dockable they could move and size nicely with the application window and retain relative positioning.
With stackable docks could then make each tab of Tool & Paint Settings and each palette edit tab a separate docker so they can be unstacked as desired for easy access where there is sufficient screen real estate.
The contents of the top info/controls bar could be moved into docks to free up vertical space: editing context dock with paint mode, brush, colours and gradient; info dock with dimensions and mouse position; tile map dock with tile map info and controls.
Would still be able to place docks at top edge of window to reproduce the existing layout for those who prefer it.
Could by default stack a gradient selector dock with the palette dock for easier gradient handling and have the gradient list double as an extra colour selection interface.