I don't think that reason holds much logic - "They may have very different best possible times so let's put them on the same leaderboard" seems like a pretty random reason to do that.

When the game came out nobody really knew; now we have more knowledge we can more easily determine good reasons for doing one or the other. That is not one of them.

To add to that, I actually agree with OP; I think it's a good idea. It's all but confirmed that Pikachu is a few minutes slower, and although the route is similar, the execution is different. In addition some people own both games, and their times for one game will never be publicly visible since their time for the other is faster, which kind of undermines the player's achievement.

I created my own as a Java app. It's a little more basic but less buggy, and as I created it myself I can also extend it to include anything I want. If it's useful for others I can make the executable available and the code open source. If people would rather stick with the current widely used one then I probably won't bother with the effort :D