I would argue that even if individual captains are acquiring these ships, if they are flying them under the banner of Starfleet, Starfleet would have a say in some things.
On the topic of Jem ship/faction interactions and green alien women (and men), the Jem HEC cannot slot the 3 Orion deployables. (Was that a pretty segue or what?)
As a Trek fan, this is jive because they are small so they're exactly what you would expect from a smaller hybrid carrier.
As a player, this is jive because 2 of them are fast enough to keep up with the HEC. Further, the reason to slot a pet is CC due to damage being meh. Without the 3 Orions the only CC left for KDF is siphons, which you run at the cost of your self-respect and the risk of emptying FvK queues.
As a customer, this is jive because these 3 have never been restricted in the manner of the frigate level hangars (yes I have purchased all 3). There was no expectation they would be, so customers who purchased both find themselves unable to use them together.
Were I a shareholder, this is jive because many Jem HEC owners have shown themselves willing to pay for things under the F2P model, but are prevented from purchasing the Orion deployables to go with their HEC.
The issue has been raised by players here and in bug tickets, but nobody is saying anything. Please say this is a coding oversight because the KDF didn't have a HEC in the past.