The problem that I have with Mobicreator is that the files have to be converted from a format other than prc in order to set the metadata. So, if you have a prc file, you can't load it into the creator and change the metadata. At least, I can't get that to work.
You're sure right about the messy directory file system on the Kindle. It drives me crazy.
I hope that they will address some of that in future software updates.