Daystrom Institute

It should be considered no different than scanning for errant microbes/viruses/changlings. Not to mention, there should already be a detectable difference in phase variance by merely being a body in another point in spacetime (updated info not reaching all known outposts/ships notwithstanding).

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.