Interesting, I never noticed this. Might be something to consider in the future, however like you said, I first would like to present the extended trilogy in the best way possible as it was released.
That is fair enough I figured as much. The other thing to look out for that you might be interested in is the Cannes preview a 26 minute piece which was released on the ultimate box set recently. This contains some extended and alternate shots especially for the Mines of Moria battle. It is in very good quality also as in perfect HD and finished professionally.
Good luck with this though. I wish you all the best.