Yeah, the transparency color
usually doesn't matter. But it matters for all combos on layer 0. That's the only layer that shows them, and sprites always omit it because they're above layer 0.
Personally? I hate seeing that godawful pink, whether it shows up in the quest or not. >_< Rather, I've color-coded CSets 6 through 11 with light colors in the transparency slot, which makes it easy to see at a glance which CSet I'm using.
![icon_razz.gif](style_emoticons/default/icon_razz.gif)
For instance, Pure CSet 7 is light blue, CSet 8 is light red (technically pink), and 11 is light lavender.
It's usually best to leave black as the transparency color for CSets 0 through 4, and maybe for CSet 5 depending on what you're using it for.
![icon_smile.gif](style_emoticons/default/icon_smile.gif)
The exception to this would be Gameboy tilesets, where they usually use that wierd light tan as the transparency color -- part of a strange attempt to keep it "authentic." It's a good example of a case where it need not be black, even if it's the
only example.