The engine cradle, has the steering gear, lower engine mounts, and the control arms attached to it, and not a whole lot else. From the sounds of the estimate they're replacing all of the commonly damaged parts. Most likely they're replacing the engine cradle because it's bent where the control arms mount, or it has cosmetic damage to the weaker front section that doesn't support anything. I've yet to see one bent far enough to affect the engine or transmission, that part of the cradle is as strong as the unibody, hitting hard enough to damage that portion would bend the frame and likely total the vehicle.
Now, the EGR valve, is by far the most common failure on these vehicles, while yes, the jolt could have damaged it you're going to have a hard time proving it to the adjuster due to it's failure rate alone. The transmission, as long as you didn't drive over anything substantial there shouldn't be any damage related to the frontal impact as it's located in the middle of the car, more or less between the front seats.
It look like they've made a pretty thorough estimate, though, for your peace of mind I'd have them lift it so you can see for yourself that there's no damage to the engine, transmission, or transfer case.
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The valve being stuck open likely is related to the accident then, it's going to be a matter of convincing the adjuster that the problem didn't occur until the accident, which is going to be very difficult with the adjuster already having it in his head that it's not related. Unfortunately it's a problem part, making it that much more difficult.