It is actually still 8-bit aligned with padding - we are talking about a system with a 68000 and Z80 here. The way the graphics systems of the era accomplished

It is actually still 8-bit aligned with padding - we are talking about a system with a 68000 and Z80 here. The way the graphics systems of the era accomplished color depths like this was generally to do one of two things: 1. draw them in "planar" mode(multiple bitmap layers of a more convenient depth like 1-bit, then composited together into the full image) vs the "chunky" mode we are familiar with(all color information packed in each pixel of the bitmap). Planar graphics are much less convenient for ordinary drawing tasks, but they allow for a tradeoff between memory usage and fidelity. Put they ease a few kinds of raster effects if you carefully use your palettes. This is what the Amiga OCS had, and VGA in many of the custom modes. 2. Allocate the colors to sprite and tile hardware with limited palettes, so that you can achieve "n colors visible" by carefully combining all the different elements. Each element might be able to sample part of the 9-bit space with a palette of 4 or 16. In the case of the Genesis VDP your limit is ~64 colors visible of 512, with the special Shadow/Highlight mode allowing more. This is not as big of a limitation as it sounds like since the low resolution graphics of the time weren't suited for detailed color values: 4 is enough to do a shadow/midtone/highlight, and 16 allows for substantial color ramps with multiple hues.