not really. It will be far better setup for towing. How many full size diesel trucks are ordered or can even be ordered with a manual these days. The new JL has larger axles and more engine options than the exiting JK. The JL had a larger bed but if you need more than just buy a full size truck. Two totally different markets. I will take the slightly smaller bed with about 7500lbs towing and still be able to lower the soft top and add accessories that no truck will be able to match. The new JL Wrangler are going to be hitting a lot more market segments than ever before. I think you will be pleasantly surprised at the final product.
I have a 2003 ram diesel with a 6 speed manual with an 8 ft box and my son just bought a 2017 ram diesel with a 6 speed manual but it has the shorter box. The dealers don't like bringing them in as a standard transmission as they are not as saleable to the general public. When my son got his only one person at the dealership could drive a standard and that was a mechanic in the back shop.