I don't know if they are still doing it like they used but it's possible the dealer plans to use one amp for ALL speakers including the sub. That is how my boat came from the factory but it's quite a bit older.

Also, I'm not sure ive seen a factory box install? It could be they are throwing a free air sub in there.

You need to find out what exactly the plan is for the entire stereo if you agree to the upgrade. How many speakers you have (the model) and how they will be powered (amp model).

Just an FYI, if you hope to hear the music at wakeboard/kneeboard/ski distance then you will want to look elsewhere on the tower speakers. Unsure of your goal on tower speakers but I figured I'd mention it now so there is no surprise later.