1. The new folder is created so as not to overwrite the original file with the same name. There is no way to turn this off. It is not something that Map Pilot Pro controls.
2. All file naming is handled internally to the camera. If you are doing a mission that will require over 1000 images there really isn't a way around this. All files being uploaded to Maps Made Easy need to have unique filenames. There are quite a few threads on here about managing this.
It is an extra step but isn't TOO bad to manage.
At least now the numbers go from 0001 to 9999 before starting a new directory. Some older aircraft only went up to 999 which made for a lot more shuffling around.