I think Dropships have something extra added that AoW era Dropshuttles didn't have that no longer allows them to be inside something & must use a Docking Collar.
That said, a Warship has the HUGE bay doors to hold a Dropshuttle in it.
In the Tech Manual, we do have the Tech Level C item "Docking Collar" in the "AEROSPACE UNIT STRUCTURAL COSTS AND AVAILABILITY" table, costing 10,000 C-B. That could be the reason.
Other reasons could be mass and cost-related:
A Dropshuttle bay masses 11,000 tons, and can carry up to 2 Dropshuttles (each massing no more than 5 ktons), which would be ~5500 tons per Dropshuttle. A Docking Collar only needs 1000 tons per Dropship, and can handle Dropships over 5 ktons in mass. So just on a tonnage basis, you have an advantage to using Dropships.
For KF costs, I used the Strategic Operations Corr 2nd printing (wish the credits page had a date on it to reflect the last time errata was added to it) to compare a 500 kton vessel's compact core with zero Dropship capacity vs a 500 kton Jumpship core with 10 Dropship capacity. This did not include any other features, just the KF core itself.
500 kton Compact core:
500 kton Compact core: DS Capacity = 0, Integrity = 12, Sail Mass = 55 tons
Drive Coil 60,000,000
Initiator 25,000,000
Controller 50,000,000
Tankage 600,000
Sail 2,750,000
Charging System 500,000
Compact Core increase 555,400,000 (the above costs are multiplied by 4, and added to the prior total to get a final multiplier of 5: 4N+N = 5N)
KF Support Systems 2,000,000,000
-------------------------------------
Base cost: 2,694,250,000
Warship cost multiplier: 2
Final Warship cost: 5,388,500,000
vs
500 kton Jumpship core w/10 Dropship capacity:
500 kton Jumpship core: DS Capacity = 10, Integrity = 10, Sail Mass = 97 tons
Drive Coil 810,000,000
Initiator 75,000,000
Controller 50,000,000
Tankage 500,000
Sail 4,850,000
Charging System 2,500,000
Compact Core increase 0 (no need to multiply the above costs)
KF Support Systems 500,000,000
-------------------------------------
Base cost: 1,442,850,000
Jumpship cost multiplier: 1.25
Final Jumpship cost: 1,803,562,500
So in addition to being able to use Drop vessels over 5 ktons, you also have a KF core that is ~1/3 the cost for the same capability.
I am not considering scheduling in the matter, as even though it takes a KF vessel ~1 week to recharge while a Dropship or Dropshuttle could take 3 weeks to make a round trip to a planet, this is true for both compact-core Dropshuttle carriers and Jumpship core Dropship carriers. The Dropshuttle carrier would just release the Dropshuttles at the Jump point, and while the Dropshuttles headed in-system the Dropshuttle carrier would recharge and pop back to pick up another batch. Jumpships would perform the same maneuver.
I'm not so sure the cargo bay doors on a Mammoth are even large enough for a Union to enter.
Mammoth dimensions
Mass 52,000 tons
Length 277 meters
Width 277 meters
Height 170.6 meters
Union Dimensions
Mass 3,600 tons
Length 81.5 meters
Width 81.5 meters
Height 78 meters
The door on the Mammoth in the picture from the TRO is pretty big but its no where close to 80m tall compared to the height of the ship.
For a Union, using that door is not likely. But for the combat Dropships (i.e.
Achilles) you have LWH of 125m x 38m x 23m, which would be barely enough to stack 5 vertically. Of course it helps that the Achilles has about ten times the density of the Mammoth.
As to putting Dropships through the door, the Mammoth would have to be re-engineered to handle the large 'single' cargoes, instead of its normal containerized cargo. Since containerized cargo can be transferred 5* as fast as non-containerized, no regular Mammoth would want to deal with this. Hence the custom Dropship belonging to a unique mercenary unit.
