Test 1: Wood
Using the manual method kept more of the dark information such as the cracks. This could probably be made better with a little more work to balance levels, however this may be a desired look for the material type.
The ShaderMap results have more colour variation as the dark areas are better filled with colour information which better fits the definition of an albedo map.
Close up the difference in dark areas can be seen, but at a further distances the difference is barely noticeable. Other than the dark notch detail which looks washed out in the ShaderMap version, the maps look very similar to each other but for the use of this texture I do prefer the results of the manual process.