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I wouldn't think so. I don't think it'd be too hard to reprogram it to use the red key. Alternatively, I think you can also just swap the key internals. I did this once and it seemed to work fine. Some locksmiths can also reprogram keys to use a particular ID (in this case, the one that the trackey uses).
I don't think it's a deal breaker..........The Boss is potent enough without it.......and there are tunes out there if you want anymore of what you think you're missing. I always thought it should have been offered as an option right from the factory..................
If the buyer is a collector, it probably drops what they'll pay a bit. Otherwise, no big deal.
Haven't done it myself, but I believe HP Tuners software can access both "sides" of the Copperhead ECU, so you can program different tunes for the silver and red keys. TracKey is essentially using the MyKey "valet/teenager key" feature, but makes changes to improve performance rather than limit it. There's a constraint on the amount of difference between the two tunes, though -- the Copperhead PCM has limited storage.