I'm not so sure.
The "original" layout that Lee and others are posting has several alleged indoor show scenes, but since this is a rollercoaster and must maintain a certain amount of momentum between the lift hills, you would have needed to move past them at a certain clip. This means that any details in the scenes wouldn't have been as important as you would probably just whip by them, Big Thunder style.
Instead, Disney went with one big, long show scene with a slow, metered pace, so you can enjoy the nuances of the figures and their animation. To my way of thinking, this makes Mine Train more of a dark ride/coaster hybrid like Mummy and less of a themed Runwaway mine car coaster like Big Thunder, ie. it makes it more unique and more interesting. Overall ride duration might actually be the same when you figure in the actual speed of the train in these parts.
Now, whether this was a conscious design decision based on how nice the final versions of the figures would become or simply a cutback due to cost overruns (or other design considerations like envelope clearance), I don't know, but if all the "original" track layout offered was some additional low-speed helices and blow-through cave portions, I'm not particularly sore for missing them.