I've known this was how it works for a long time, but personally I find those extra colors far to difficult to access for it to matter. And since they're GUI colors, you can't customize them, right? If Cukeman is making his own palette intended JUST for 8-bit tiles, he will already have a huge number of colors represented.
Boss C-sets get loaded into C-set 14, then if there are more than one type of monster that uses extended C-sets, 13 and 12 are filled as a result.
So THAT'S how it works. I had wondered for quite awhile how ZC handles boss palettes without overloading the 256-color limitation when multiple extra sprite palette CSets are required at once. I wonder if it's possible to overload the palette with more than four different extra sprite palette CSets on the same screen? I expect ZC would either have display flaws, or it would crash..
Yes, this is correct. Many tilesets have duplicate CSets in the extra sprite palette, for simplicity -- for instance, most tilesets have a copy of Ganon's CSet in the slot for CSet 11, even though he doesn't actually use CSet 11.
Personally, my quest's Gleeok and Aquamentus enemies use colors that aren't available in the main palette. I don't remember whether I included those CSets in the public tileset.