I prefer the 540 also, but there are some considerations for going 1000. The biggest is weight, the 1000 is much easier to handle. Many larger tractors only come in 1000 so that will be a consideration in future tractor purposes. The cons are you can expect the 1000 to wear out faster since it is making two revolutions for each on revolution of a 540. The lightness of the shaft should not be much of a consideration as far as holding up since you can put twice the torque through a 1000 than a 540 of the same size. So theoretically a 1000 only needs to 1/2 as strong as the 540.
Why the 5x5 NH is 1500 lbs lighter is a matter of small differences adding up. The rolls are the same the pickup is the same for a standard 5x6. The 5x5 also has one less tailgate roll, I am thinking without looking. the belts are shorter and the frame is shorter. The standard wheels are smaller on a 5x5. The net system is the same as is the gearbox. The pto drive shaft is smaller though.
After a customer had 3 5x5 balers over the 10 years, I finally convinced him to go with the 560. He was in recently and said he hated to admit it, but I was correct. Baling with a 5x6 baler is much better. His problem was tractor also. It wasn't that he did not have a big enough tractor, but the tractor he wanted to use was smaller. When you are limited in the number of big tractors, you have to make decisions on where to use it. He did get a new ts3.130 or 140 so he uses that on the baler now. That would compare to your Kubota, JD. He does a lot of custom work in the area so he gets on some steep hills, I seen it. FWD is a must in those cases and that size tractor.