So there is a town called Covenant that gives a test (S.A.F.E. test) before you can enter and trade. The test is basically the old F3 vault questions. The trading prices in town are low to encourage more traders to come through.
Long story short, the settlement is a front for an anti-Institute group that uses the test to identify potential synths. Once people are identified as a potential synth (by failing the test) they are later kidnapped (killing others if needed) and taken to a place called the Compound. At the Compound they are tortured and repeatedly given the S.A.F.E. test to gather more data and evaluate if that person is actually a synth. Then the person is ultimately killed and autopsied to determine if they are a snyth.
http://fallout.wikia.com/wiki/Subject_12_baseline
http://fallout.wikia.com/wiki/Subject_12_testing
http://fallout.wikia.com/wiki/Subject_12_debrief
Now for some numbers:
The current S.A.F.E. test "fails" 28% of the people that take it. This means they are identified as potential synths by the test. This is not the false positive rate but the
entire positive rate as noted by who they are testing and the note about the ghoul being a definite false positive. Doctor Chambers will reinforce this in a bit.
http://fallout.wikia.com/wiki/SAFE_report
At the Compound you can get these dialog gems from Doctor Chambers.
https://fallout.gamepedia.com/Roslyn_Chambers'_dialogue
So she appears to be willing to fudge numbers to make herself appear more just depending on her reaction to the PC.
The false positvie rate can also be learned from Doctor Chambers through dialog.
In other words, 18% of the people they kidnap, torture, and kill are actually synths. Or 5% of everyone they test, ignoring false negatives which the Compound does for some reason (because they are fanatics). This is assuming she is not lying and the number is actually lower than that.
And in her best outcome scenario the test will still incorrectly tag people as synths the majority of the time. And remember that the only way to ultimately verify the test is to kill the person.
Now the fun part:
The Railroad who moves rescued synths out of the Commonwealth primarily does it using caravans and traders. The caravan that got hit to start the quest Human Error belongs to Old Man Stockton, a Railroad agent who manages Railroad runners. Checking the S.A.F.E. report Mr Tims is also mentioned; he is another Railroad runner manager. There is also a Join the Railroad holotape found in the trash in the guest house.
And finally there is a danger Railsign above the Compound. Which means another Railroad operative (probably killed by the Compound) made it but the information never got back to Railroad headquarters; because why the fuck would runners still be going through Covenant otherwise?
So most likely the majority or possibly all the synths tagged by the S.A.F.E. test were rescued synths being moved by the Railroad. Recused synths who got mind wiped and don't even know they are synths like Amelia.
You can get this dialog if you are in the Railroad and cut Honest Dan out of the loop:
https://fallout.gamepedia.com/Old_Man_Stockton's_dialogue
Which brings me to my final idea. With the Railroad moving a high number of synths among traders and caravans it is possible the S.A.F.E. test does not even work (hue hue hue). It is just noise that the Compound thinks is working because their paranoia and fanaticism need it to work. They base their test on the assumption that synths do not have true feelings but the game tends to sell you on the opposite especially in regards to escaped synths/Valentine/Danse etc..
So I killed them all. Even poor Talia, she deserves to die.
And I did not make this post to justify killing Talia because I cannot get her working as a proper settler using mods and console commands after wiping Covenant.