I think you misunderstand the pack:
The pack gives you the Cyclone MT, the P-72 Archimedes Emerald, and the Ursa Fortuna, along with the Constellation Phonix Emerald, as you noted. However the Constellation Phoenix Emerald also has a standard P-72 Archimedes as a SNUB fighter fitted, and a Lynx Rover for the vehicle\cargo bay. This means that the pack contains the following individual ships\vehicles: a Constelation Phoenix (Emerald), 2 x P-72's (One normal, one Emerald), A Lynx Rover, an Ursa Rover (fortuna), and a Cyclone MT.
The reason for this dates back to the original Constellation Phoenix Emerald's release (A time before "paints" were implemented and changing the "skin" for a flyable ship meant releasing a new "model" of it with slightly different name), where only the base ship was given a new colour, and not the snub. Some time after this, they decided (were urged by backers?) to release a P-72 and an Ursa Rover (as the Ursa is the "loaner" for a Lynx, which had not yet entered development) which would match\compliment the Phoenix Emerald's colour scheme. These were released individually to allow for owners of the Phoenix Emerald (as well as anyone else) to be able to buy them, as well as in a pack with it - They couldn't change the "Constellation Phoenix Emerald" to have these in place of the "base" versions without affecting owners of the original release(s).
The 890 Jump, Carrack (standard and Expedition), 600i Explorer, and Constellations Aquilla, Andromeda, and Phoenix (normal and Emerald), although listed as ships, sit somewhere between being classed as a "ship" and a "pack" - They contain additional vehicles\ships which should make up a part of the total listed price, but these additional ships\vehicles are not "upgradable" via CCU's like a standard ship\vehicle.