But as I said, most of the onscreen evidence shows that the Doctor can only be transferred rather than copied. Sure, you can argue in the abstract that something is plausible, but if the actual facts presented in the show depict a different scenario, then all we can do is accept that reality and try to explain it.
At the risk of drawing attention to the elephant in the room, unless information is now using the transporter, computers "transfer" information by copying it and erasing it from where it was previously. It's possible computer technology works completely differently in the 24th century but, technically, the Doctor is being erased and copied everytime he's moved to a mobile emitter.
The thing is, I'm entirely comfortable that the Doctor can't be copied without specialized software and THAT'S why the backup was necessary and it became such a hassle to recreate him afterward.
Still, you're right, I may be overthinking this like Babylon Five's "life transfer" device. Vitalism is just true in B5, accept it.
Why in the world would it have to exist? That doesn't make any sense. In nature, many processes are regulated quite well by local rules. There's no central brain telling the molecules in a snowflake what overall pattern to form; they just connect at certain angles to the molecules immediately around them, and the operation of the local rules produces the emergent result of a higher order of structure. Same with an ant colony -- the queen isn't issuing orders to each individual ant, just churning out more ants that follow a limited set of local rules for interacting with their neighbors, rules which interact in such a way as to spontaneously produce higher orders of organization and complexity. Ditto for the neurons in our own brains, for that matter.
Besides, again we come down to raw numbers. Slipstream drive may allow travel to more distant worlds, but the actual number of worlds that could be visited, settled, or allied with during the lifetime of a typical political entity or civilization would be finite. You'd still be settling/contacting the same number of worlds per year, they'd just be spread out a lot more widely. There just wouldn't be time to contact and interact with every one of a hundred million civilizations in under a few millennia, no matter how fast your drives are. There are simply too many of them.
My rationale for this is basically the better travel times get, the more free-flow of information occurs, and the more cultural uniformity occurs across the universe--the smaller the universe gets. The Federation eventually covering the entire galaxy just seems to be a natural result of the fact that once there is "you can cross X amount of space instantly" you'd need a regulatory body to handle questions of soveignty, planetary rights, appeals, and so on.
If everyone also agrees on X principles, is it more likely the universe will be six different "Federation of Kronos, Federation of Gorn, Federation of Romulus" or one gigantic Federation?
But yes, your correct, there is no rationale Earth analogy for what I'm proposing and it's unlikely we'll never know since we'll all probably be Borg or extinct by the time such a question would be pertinent.