The tractor beam goes down directly below the UFO. It's a bit hard to see when it's turned off, but it's still there.
The cows do count! All of the objects you've collected get pushed out in the explosion. It's hard to tell what they are because the camera is a distance away, but I promise you they're there. I even used the exact same game objects that were collected.
When the train 'crashes', all of those objects are moved a bit in front of the crash center, with slight randomized offsets in each direction, and then they have an force applied to them to simulate the explosion. So it's randomized, but within some pretty tight limits so most of them should be aimed towards the buildings.
The 'secret' with the batteries is that for each one you collected, the game increases the simulated mass of the launched objects, so they're more likely to actually knock over the buildings when they hit them. If you collected all of the cows and trees but none of the batteries, the explosion would launch a ton of objects at the buildings, but they'd all just bounce off because their mass would be so low compared to the buildings' masses.