My knowledge of Microsoft Windows is quite limited (even if I used Windows 95 and NT4 for several years), and today I looked for documentation to check that we add the correct Windows partition to bootloader. I was quite surprised by Microsoft naming.
To quote wikipedia:
In Microsoft Windows, the system partition and boot partition refer to:
This naming is indeed the one described by Microsoft.
So, system partition is the one containing boot files, and boot partition is the one containing system files. I really can't understand how they came to this naming...