Hi thanks for such a clear and detailed explanation of the problem! :)
I've been doing a lot of work on the beatmaker recently and I think that this problem is already partly solved in the development version when making beats. (It doesn't allow you to place two notes too close together) although the problem with the random beats still exists. I'll try to take another look at that before the uploading next update.
I'm holding off on updating the game for a while as I still need to round a few things off before it's ready for people to use, so it might be a while before you can try out the changes.