Of course SpamSieve can use the system color palette to let you pick a color. But that’s not what you’re asking for. You’re asking for SpamSieve to tell Mail, as it’s filtering messages, to assign custom colors to messages, and for Mail to then remember those colors. As to Apple, you would be surprised at how much they don’t make accessible to third-party developers. There are lots of features that you see across many apps, and which you might assume are part of the frameworks, but which each developer has had to reverse-engineer or write from scratch.
The interface that SpamSieve is currently using to set message colors is supported by Apple, but it only supports Mail’s built-in list of colors. I’m not happy with this or with the color choices, but that’s how it is.
Some versions of Mail do seem to have an internal means of assigning a wider range of colors to messages, and it’s possible that I will be able to reverse-engineer a way to use this. (It’s also possible that the mechanism is there but that Mail is designed in such a way that it can’t be reliably used from plug-ins such as SpamSieve’s. After all, Mail was not designed to be expandable, so plug-ins must tread lightly so as not to mess anything up.)
If SpamSieve ever does support using finer gradations of color, my preference would be to use gray or brown, as you want to ignore the spam messages. Brighter, attention-drawing colors should be reserved for the messages that you find important.