Given the present relationship between the UP and Metra, I'm a bit surprised they agreed to allow the CNW logo to be used. They couldn't really argue the colors since UP didn't even use the right shades of yellow & green on UP1995...
Also given the number of UP painted lease units still roaming about in yellow/grey/red, I don't know that they could seriously challenge the color use. Metra isn't in the business of freight railroading, and UP isn't in the passenger business, so it might not be worth pursuing. As much as I'd love to see a F40PH show up in yellow, it's probably not going to happen now that the Hiawatha unit was done. But if they do a BN themed unit (rumored) in addition to the CB&Q, perhaps I can hold out hope.
The RTA unit is long gone. That was always planned to be temporary and applied as a wrap for the anniversary vs. paint.
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