It is important as different meters react to different colors differently. Same goes for metering through colored filters. I remember seeing somewhere in a book the color sensitivity of the Pentax Spotmeter. It certainly was not linear with respect to color and that was taking the relative reflectance of the color materials into consideration.
However taking your question into consideration if you metered a yellow object in the shadow you would still underexpose by 2 stops from what the meter said. Same goes for the indigo object. The meter will give you two very different readings depending on which object you metered. In either case underexpose by 2 stops. This will place whichever object you metered off on Zone 3.
Now if you were able to find out that your meter gave a +3/4 stop error when reading yellow you would have to take that into consideration when determining your calculation.
In the real world I have never really worried about specific color sensitivity or lack thereof.