I think this would all come down to how you define the parameters of the comparison. I would think it would have to be off the shelf mass produced to be realistic. Then you would have to label them "Vendor A" and "Vendor B" and let the blind "taste test" begin.
The first problem of course is the visual differences in quality (materials and manufacture) from gen to rep. However, these are details that I would wager only about 5% of consumers would notice. So it is difficult to say if this would have an effect on estimated value or not.
I would think the larger issue would be longevity. We all know you get the odd DOA or DAAFD (Dead After A Few Days) with reps. Here it all comes down to probability of failure. With gen it is possible but very unlikely. With the rep...who knows. Even after failure support and repair is the key. With a rep where do you take it? What to do? The gen has infrastructure, parts supply, etc. so getting support is no problem. So, while on the surface the value of both pieces may look the same, the story after a problem would likely change. I would compare this to buying a Toyota vs. a Yugo.
Next is design. Without the gen in the beginning there would be nothing to rep. So one of the two companies has to bear the burden of design and development. This can be costly. How much I suppose depends on the details of the design. But again it adds to the cost of the gen.
Some have mentioned modded versions of the reps to help level the playing field but in this case you would have to account for the costs of time and materials of the modder and the mods performed (some of which are gen parts ie: concepta IWC's) Also, this would be on a one to one or singular basis. The idea is that these need to be mass produced. If that were the case just think how many conceptas we would need to keep up with demand!?! Conversely if demand is high and there is only one concepta (which of course we know there IS only one ) his time would become very valuable. So for me this would invalidate any modded reps from the comparison.
So in the end there are many aspects that go beyond just the superficial review of appearance that add to the cost of the gen. How much this is worth....hard to say but the market has already spoken