...Criss, I hate to be the negative person here, but build for lore, not for the poor functionality we have now. Don't base every off of the honestly dreadful docking AI, or what they WILL be able to do. Base it off of what makes SENSE. They MUST be able to connect to each other if they're in the same faction, should have some way to dock to each other if they're allies/trade partners, and might not only if they're combat vessels designed to never interact with the other faction(s).
Call it what you will: Lore, realism, OCD, whatever. But just saying "Because game mechanics don't allow it" is a poor way to design for a game that is ever-changing.
That said, it's probably time to start refitting some of my vessels...the ones that relied on the game mechanics that existed at the time.........so all of them, in fact. Anyway.
Hypocrisy to victory!