The trick is really about concatenation. If you look at the nodes in the transform panel, some have a small letter c in the corner. This means that Shake will compute multiple transforms before generating an image.
So what you need to make sure of is that the main zoom node is directly linked to each of the individual scale/transform nodes that you use for alignment. However, you need to have a composite node somewhere but putting it in between breaks the transform concatenation, which is why you are seeing image quality loss.
So, I would say the easiest way to set this up is to use a multi-layer node (remember this works the opposite way round from the over node in that backgrounds come first). I tend to use Move3D and multi-layer nodes all the time because you don’t lose any processing speed and the extra functionality is there when you need it. You can use over nodes if you prefer though.
So yeah, attach image 1 and two to the multi-layer node and scale the closest one (e.g. street-level) down using a transform node. Now copy this transform and instead of pasting, right-click and choose edit > paste linked - in the image, this is called Move3D2_clone1. Then insert it onto the second image by holding the n key. You will see this has scaled down the further out zoom too. We need to scale this back up.
So add another Move3D node above it (Move3D1 in the picture). It’s important that it’s above because you need the center point of the common scale node to be in the same place - this can be confusing relative to a layer based app or 3D app because they work from top to bottom, parent to child. In Shake it helps to think of the source nodes as the children. So now on node Move3D1, scale the further out zoom image back up. notice that although you are scaling above 1, it won’t lose quality. Get image 1 and 2 in alignment and repeat for all your images. Your tree should look something like this:

The pink circled node Move3d2 is the node you scale from 1 to 0.003 or whatever, since they are linked, you just need to animate the original one. I actually found this process out the hard way because I tried to do the same for a project a while back and I seriously wish I’d had that tutorial. Even a quad G5 with 4GB Ram chokes if you try to scale a 2000x2000 res picture up by more than about 5 or so. It just kept crashing the render.
Just hit i to ignore the images you are not aligning but be careful when adjusting the upper Move 3D nodes because they are not all parented like in the AE tutorial so you basically have to align 2 to 1 and then scale the main node down and then align 3 to 2 but do not adjust 2 again and so on. I guess you could have multiple linked nodes but it gets pretty messy. If there is a better way to do it, someone else is welcome to chip in but this setup seems to work and the composite tree is simple so I hope it helps.