The one on the seat is for a d-lock iirc. The two under the seat are for the toolkits, my old fazer only had one but my new one has two...
The strap under the seat is for the D-Lock you can see where the lock will fit within the structure of the seat - one or both under seat compartments are for tooolkit(s), if one is missing a toolkit then it is used for storage. Any reason why this is so important to you or do you suffer from OCD?