It's easy for us to understand that The Doctor is a sapient being.
After all, he acts like one! He's got a slew of odd personality quirks, balances irritating behavior with kindness and sympathy, behaves in a similarly slightly erratic manner as most of us flesh and blood creatures, and responds to difficulties with every appearance of genuine emotion. It's extremely easy for human audiences to look at the early seasons Voyager crew as bigoted for their slow acceptance of him as a "real" member of the crew, and react very harshly to later challenges to his personhood from people outside of the crew. It's not uncommon to see that behavior referenced as proof that 24th century people are no more "enlightened" than the obviously flawed people of today. And maybe they aren't; that's not my topic for today.
But the element I think that argument is missing is something these 24th century people have been exposed to all their lives, and we in 2024 have only begun to encounter: soulless, unconscious entities capable of impressive imitations of a real person.
24th century holograms appear as perfect copies of physical humans, with perfectly recognizable voices, normal human mannerisms, and convincingly human speech that responds naturally and automatically to nearly any expected or unexpected input. Any of us unknowingly tossed onto a 24th century holodeck would be totally convinced that these people projected around us and interacting with us are as real as anybody we meet today: nothing they do will clue us in to the fact that we're interacting with philosophical zombies.
Most of us first encountered something like this when ChatGPT and it's ilk suddenly got really good and easily accessible just a couple years ago. Suddenly a computer could create text that read like a human had written it, responding to context and occasionally interjecting very human behaviors (like making up answers to stuff it didn't know, and attempting to gaslight anyone who called it out for being wrong). A shocking number of modern people seem to genuinely believe that these bots show real consciousness (even some who really ought to know better). And it's not hard to understand why, when these bots can spoof every text-based indication of humanity that most of us look for.
People of the 24th century have spent their entire lives interacting with bots that smash the Turing Test even more thoroughly, and on every level imaginable. They can walk onto a holodeck and spin up a person from scratch who looks, smells, feels, and sounds completely real, who talks coherently and shows perfectly ordinary physical mannerisms. And they also know, with ironclad certainty, that these creations are no more human and no more alive than a tricorder or a hyperspanner. Just about all they have to definitively prove if someone is real or not lies in if they can exist outside the holodeck.
Enter The Doctor. He's very definitively a hologram. When first activated he's no more real than any other holographic creation, and only slowly grows in unanticipated ways which slowly convince his crew that he's become something more than that. This process is slow, but it's actually a bit of a surprise that it happens at all. Excepting Kes and Neelix, everyone on Voyager is quite accustomed to holographically generated people who act human but are purely a facade. That this very reasonable prejudice could be overcome at all should be seen as a triumph of empathy. It's not at all surprising that the people back home on Earth aren't buying it, and can't even be persuaded beyond a bare minimum threshold of plausible uncertainty.
I theorize that people who are growing up right now in an environment of very convincing AI chatbots will find it easier than we did to recognize holographic beings in Star Trek shows as sophisticated extensions of those internet bots, and will mirror the slow acceptance by Voyager's crew that The Doctor is something more than that.
So what does that mean for us? What do we do as more of our instinctive indicators of another person's humanity are effortlessly aped by machines? This is a difficulty which Star Trek shows had only begun to grapple with, but it's fertile ground for future episodes and undeniably a relevant question for our day.
Transporter clones appear to be vanishingly rare. We're aware of two (Thomas Riker and William Boimler), and the circumstances around Thomas Riker's existence were clearly unheard of to any of the people investigating. Clearly this is not a thing that transporters normally do, or are even capable of outside of extremely unusual circumstances.
It also seems pretty dystopian to require the insertion of artificial genetic markers to make a person more easily recognizable. Would we expect "normal" identical twins to be treated similarly? Or actual clones?
I think the larger lesson on this incident from Starfleet's perspective is that they need to beef up their internal security practices. Big shocker, that. Thomas Riker is neither the first nor last person to successfully impersonate a starfleet officer and cause major troubles in doing so, and most threat vectors can't be solved by preemptively identifying likely perpetrators (such as this likely very offended transporter clone) and modifying them specifically to make infiltration more difficult.