One of my our customer have the same issue as you. I'm so confused.
When you say
"one of my our customers", I'm assuming you work at Sprint?
If that's the case, and you're confused, that's a little disheartening. I think it's important that sales/customer service reps at least be able to explain how the partitioning works...and it's not like it's that complicated either.
If you look at any memory card, none of the cards have the "total" amount of memory that it says. When you place a blank memory card into a card reader and connect it to a computer, you'll see that the amount of available memory is always lower than the total amount.
With a cell phone's "internal" storage, some of that internal storage is used for functionalities of the phone. So, in this case, to re-hash what has already been said, the Photon is partitioned accordingly:
3gb / 16gb - Apps Only
8.92gb / 16gb - Internal storage (apps moved to sd, which go in here, or whatever else someone might want to move)
4.08gb / 16gb - Non-accessible memory used for different functions of the phone (although, can be accessed via ROOT).