"all other organisation is down to the application using the drive (i.e Windows, Linux)"

I'm afraid this is also incorrect. The MBR and partition table operate below operating system level which is why it is possible to have different operating systems in separate partitions of the same physical disk.

Most (all?) operating systems provide some means of accessing the partition table (eg fdisk) and some means of writing the MBR in the first place (eg format x: /MBR), but the function of the MBR and partition table is independent of the operating systems installed in the disk partitions.