It's a bit hard to quantify why the non-stock seats are generally better, but here's my best shot.
Foam - often the stock foam is a bit squishy. All of the after market seats brag about their foam. Ultimate says their's is formulated for a "progressive squish" (my word). Corbin has a very firm foam that adapts to your butt, takes a while to break in.
Shape - if your Corbin seat doesn't suit you, they will reshape it once for free. On the RT I hate the ridge behind the driver (cuts into my lower back), and my Ultimate has a shape that overcomes this. I just fit better on my Ultimate than the stock seat. Ultimate says "you sit in it, not on it" and while I think it's true, it is advertising. On my Honda Shadow, my back was killing me after about 3 hours but once I got the Mustang I could ride all day.
Accessories - Corbin and Ultimate both offer a fuel door, which is a NICE enhancement. Doesn't make you sit better but still very nice.
You're correct - if you buy a new seat, backrest, rear backrest, and rear armrests you're out over $1k so this isn't a trivial farkle. However, the RT is a touring byke, and small adjustments make an incredible difference after several hours of butt/seat contact.
Ultimate allows you to try a seat and return it within 14 days if you don't like (you pay for return shipping). Mustang has always offered a similar deal, Corbin and RDL don't. This is on the theory that you can't judge a seat in a few minutes, it takes several hours of ryding.
My best endorsement for my Ultimate seat is this - with the stock seat I felt uncomfortable a lot. With the Ultimate, I just don't think about the seat.