So my question is with the new folder model introduced here does that reflect multiple JPEG folders as multiple RAW folders? Or would it still overwrite the DNGs like I experienced?
If you choose the "A/DCIM" option then all the files go into a single hard coded folder like A/DCIM/100CANON etc, so a counter reset will cause existing files to be overwritten.
If you choose the A/RAW options, then folders should be created the same as in the DCIM directory, so it should behave the same as withJPEG. Either of these could be broken if the ports image counter code is broken, but otherwise should not overwrite existing files.