Here’s a suggestion for the GFUI: Provide a way to turn off the “Your design has a lot of colors” message. Preferably by a “Do not show this message again” check box (like the many warning messages in Adobe Illustrator, for example), either on a per user or per design basis. Or even make it go away all together; it’s pretty redundant since you can easily see that there are a lot of operations by looking at them on the left side of the GFUI.
They could make it a toast notification, that way it’s not intrusive. I agree though, having a notification that can and will be ignored is bad UX.