It will, for a few reasons.
First, the seller has to pay the price in time to grind up the spiritbond. Time is money, so this will affect the price accordingly. Pretty straightforward so far.
Second, a particular piece of gear is not guaranteed to convert into a certain type of materia. If you have, say, five Raptorskin Harnesses, but only three of them convert into the most desired materia, those three materia will most likely have to cover up for the smaller price on the other two.
Third, even within the same tier of the same type of materia, the bonuses vary. This means that, taking our three materia from the last example, one of them may have the maximum bonus available, while another is low, and the last one somewhere in between. The price on the "best of the best" materia in this example would have to reflect the fact that only 20% of the gear converted (example numbers, of course) will actually produce that materia.
And, of course, I'm sure there are other factors I'm missing, but these are the three that come to mind.
