Multi-resolution subdivision editing means that when you make any changes to any level of the mesh and then switch to another level, those changes will be interpolated across all other subdivision levels. This applies both up the levels and down.
Example: You are sculpting a croc’s head and decide that you want the mouth to be longer. You go to level 1 where you can move just a few points to make the mouth longer. When you return to the highest level, the teeth and all other high level details will have moved to fit the changes made at the lower level.
The same works in reverse. When you make changes at a high level, the lower levels of the mesh will be adjusted to fit.
Example: You are sculpting a head and decide that you wish to add short devil-type horns. You use Projection Master and an imported head mesh to add a face to the pommel of a sword. When you move down in subdivision levels, the lower-level geometry has been updated to come as close as possible to the shape created with Projection Master. You can then continue to refine that shape if you wish at the lower level before returning to the high level for more detailing.
See how it’s advantageous for the Multi-Res features to work both ways?
Now to your “problem”. ZBrush uses the catmull-clark formula for subdividing a mesh. This includes the mesh smoothing algorithms. Why does it use this method? Because most animation software does, too. By using the same technique, it ensures that the details you create via displacement mapping will match the ZBrush version of the model.
Well, the thing about mesh smoothing using this algorithm is that the mesh will contract when it’s applied. And details get smoothed out. Take your same model and using your animation package apply a hyper-NURBS to it. What happens? Does that detail that you pointed out in your illustrations disappear? Yep! Can you superimpose the smoothed mesh over the unsmoothed one and get the same result as in the last image you posted? Yep! It’s the way that the math works. Try it once with a six-faced cube to really see some dramatic differences. 
Now, because Multi-Resolution Subdivision Editing causes all levels to be updated when you switch between them, level 1 will invariably be modified by the smoothing that takes place as you divide the mesh. This creates zero problems, however, because ZBrush also lets you import that original mesh back into level 1. By doing this right before you create the displacement map, the map is able to be calculated for the exact mesh that you are animating with, while still enjoying the many benefits of Multi-Res Editing up to that point.
Hope that helps!
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