There has been mentioned, a few times, by CIG team that there will be limitations as to what you can wear and carry while piloting. Long Arms and anything more than light armor is on the list as probably not going to be available in a pilot seat.
There have, also, been mentioned by CR and others, that you are not just going to magically pull weapons and equipment out of your pocket of infinite holding, and equip it, wherever you happen to be, hence the weapon racks and lockers in later ships.
A bounty hunter ship without either a weapon rack or a locker doesn't sound like a good plan, especially in a ship where you are working alone and chasing down bounties directly from the ship.
Now using it as air support and prisoner transport as part of a bounty hunting team, it makes sense, especially since we lack a ground vehicle with a trunk to throw a bounty into.
A ship with a similar mission profile that can replace the Merlin on a Connie makes an incredible amount of sense for a Bounty Hunter.