Quality of woods - Jems vs Prestige RG's
This question can be easily answered by looking at two guitars that are made of each, and then comparing the price. *The RG520QS (Mahogany w/Quilt Sapele top) lists $100 more than the RG520GP(Basswood) and the RG520QS lists $80 more than the RG570 & 550 which are both basswood with an extra pickup.
Maybe the figures above would prove that the price for Mahogany is more, but because of the Sapele top (which is more like a veneer), it might not be the Mahogany at all.
The S series 540's list at about $1399 vs an RG's $799-900, and they are all Mahogany, but without all of the mass of the RG body style, and the extra two frets.
Another thing to consider is the quality or grade of the wood being used.
I agree that it is Vai's choice of wood because it is his guitar and hence it is his preference in tone and weight. *
I personally prefer Mahogany, and weight is over little or no importance to me.