It makes sense. Even if it never fires at "standard" DV under normal circumstances, what if you have only loaded one round and someone kicks down your door. You turn and fire with a clickclickBLAMclick noise, DV4.
Also, if you are applying modifiers, you need to know what you are modifying. If it is ever possible to have a different modifier, it is better to start with a base DV and modify from there.
The Slivergun can never take other ammo, and the stats are always the same for Flechette ammo, so there is never going to be a different modifier. Ergo, it is worked into the stat line.