Brian, I'm not sure I agree with your statement that compacts are more expensive to operate. I'd have to compare expenses over a long period of time to make that statement, but I concede that it might be true. I've had my TC45D since February of 2001 and it has around 2000 hours on it. So, I think I'm qualified to give you some longterm owner feedback.
100 hours between oil changes is basically the same or a little longer than you would do on an automobile. If you drive a car for 100 hours and average 45 mph, that's 4,500 miles. Many of us like to change oil at 3,000 miles in our vehicles when they don't work as hard as our tractors. Since the TC45DA will only have a 5.5 quart oil change, I don't think 100 hours is excessive. What's the time on the TN? How much oil? Filter price?
300 hours is a general guidline on transmission fluid/hydraulic fluid change. I think that is a good thing to do when the tractor is new, but I'd have the oil analyzed on a "working" tractor to see if I could not push those hours beyond 400. You might find a filter change does the trick at 300 with a full oil and filter change at 500 hours. In all fairness though, NH recommends 300 hours and that's the number you have to use.
The whine from the transmission still irritates me at times, but for the most part I don't hear it or I ignore it. It's pretty much a non-issue with me. Everything you said about the loader and the ergonomics is true. The tractor has the perfect layout in my opinion with the exception of losing rear vision because of the fuel tank (and added toolbox in my case). The raised platform tractors all do not allow turning in the seat and making adjustments like the old straddle-the-running-gear tractors did.
If you are not going to need the extra 5 hp at the PTO then I would go with the TC40DA. The design of the relief valve in the transmission ensures that the TC40DA and TC35DA have the same pulling power as the TC45DA. I guess you could make the argument that the engine will not have to work as hard to do that pulling, but breaking a 10 lb test fishing line takes the same amount of pull from a 100 lb kid or a 250 lb man. That's the best analogy I can come up with. The 135 cu in. engine in the TC45DA will not be working very hard for any task you give it.
The 16LA loader is great. Last night I dug a 4 ft deep hole in the ground to bury an animal and did not have to dig much of a downramp. I think I could easily dig 3 ft deep from level ground. The loader has enough strength and reach to really get down there. It also is easy to remove and install.
With the ability to add lots of implements and up to three rear remotes, the Class III Boomers all can be real workers. The HST models are super to operate because of their ease and simplicity of well-thought-out controls. My choice would be the TC40DA over the TC45DA if I had to make the purchase based on what I know about the transmission. The amount of PTO work you do will make that decision for you.