My opinion is that the layouts are not different enough to warrant separate games. In many levels the layouts are exactly the same.
I find it funny your initial post uses GH2 as an example, there are levels with more significant differences between the two versions than this. In GH2 the only important difference is the positioning of 2 badniks, which probably costs SMS around a second. There are a couple of errors in your SMS run which to me look enough to account for the other second between the two runs you linked.