The biggest difference is the design. Higher end treeless/flex tree saddles have been slaved over for years, perfecting the design to work they way they are supposed to. I've seen some of the cheap ones have halfway decent reviews but they almost always say that they are good for the money...that doesn't mean they are great.
Not to get on a soap box about anything but treeless doesn't mean fits all. Some people (not saying you...just chatter I have heard) think that a treeless saddle will be the answer to every saddle problem they could ever have. In all honesty, on some backs, treeless can be a bigger nightmare.
A saddle tree is a very well thought out piece of tack. It distributes weight equally over the entire span of the horses back from front to back. When it is well fitted, a riders weight spreads over the area of the saddle. Treeless saddles *can* let the weight fall where it lies the most, in the seat. In the long run, it may fit your horse (or horses) really well but can still make them back sore because of the lack of weight distribution.
I have an extremely hard to fit TB and I briefly considered treeless. Once I did my research, I decided against it simply because I am a larger rider on a narrow horse. He has his work cut out for him carrying me around...I don't need to put all that weight in one little area.