No one said that every ship is atmosphere capable.
Once again, the Harbinger was for surface bombardment, and has a small range, suggesting that the Ursa HAS to be atmosphere capable. Fighters are also said to be atmosphere capable.
Those are almost certainly modified Harbingers for Ship-to-ship combat.
The Full Harbinger was almost certainly launched from a Capital ship.
Remember they had to create a whole new bomber to use the Harbinger in Anti-Capship roles.
The Harbinger used against surface targets most likely had a fantastic range as an SpSWarhead (SpS = Space-to-Surface) at the cost of lock-on time. But an Orion able to stay in position above the target long enough to do a full barrage.
When they decided to use the Harbinger against the Lucifer, they almost certainly had to modify the Harbinger.
First they created a Whole new bomber the Ursa, which is almost practically a Gunship, to carry the Harbinger.
Then, they would have had to reduce the lock-on time - in a situtation where time is of the essence, like the final battle against the Lucifer, you can't afford to spend the two-three minutes that would be required to get a positive weapons-lock at a safe distance. You need to get the lock-on as quickly as possible. So to reduce the Lock-on time, you reduce the Bomb's range.
Reduced Range means faster lock-on time.