Say, a whole brain emulation would have our experience of color, and if we get really really good at cognitive surgery, we might be able to extract the minimum necessary bits to contain that experience of color, and bolt it onto a red-eye filter. Why bother, though? What's the relevant difference?

The point of discussing the engineering of colour qualia is that it relates to the level of understanding of how consciousness works. Emulations bypass the need to understand something in order to duplicate it, and so are not relevant to the initial claim that the implementation of (colour) qualia is not understood within current science.