They are both equally fake.
The real Will Riker died.
I mean, I suppose only if you assume every transported person dies during transport. (Which has often been argued) However, Will #1 was transported normally. Will #2 (Tom) was the result of a 2nd attempt at a capture with a confinement beam, which was ultimately unnecessary & powered down, but reflected off the "alien" distortion field, and sent back to the station. Due to the mysterious distortion field, both patterns of the same man materialize in the same way. By their narrative, both materializations are miraculously the same exact man. Rather than being both fake. They maintain they're both equally real
But I do wonder if what Dr. Kingsley and her group were doing was already knowingly illegal because right up until the moment Pulaski went down to the station, she was VERY cagey and secretive. Even Troi said she wasn't saying the whole truth and recommended caution in dealing with her. It's possible they some projects, like those kids, away from the books and Federation prying eyes.
I think the intention was for her to be acting cagey about the risk they posed to outsiders, assuring everyone that there was none, when it came to the children, because she was protective of her project, but harboring unthinkable suspicions, because there was no other explanation... a lot like the
Homesoil scientists. Secretly, they know something's gone terribly wrong, but are unwilling to look into or admit it being their own fault, and thus look suspicious acting.
However! There's nothing I can recall in the episode that specifically precludes the possibility that she's acting cagey, because this is not entirely ethical or fully approved work, & since this continuity issue wants for an explanation, that fits into a reconned narrative of bans on their work, I'm willing to give it credence, at least in my head canon lol.
They must be dancing right on the line, creating from scratch rather than modifying, a technicality.
They very well could be flying a bit under the radar, using the claim that it's not explicitly genetic engineering, as such, but some other means of experimentally developing humanoid life. So, if we want to suggest there's an active ban in effect, for continuity's sake, then they are circumventing it, surreptitiously.
And that too could give the D crew a later bad impression of the Mariposans, for similar reasons, as well as the objection to being duplicated. Everybody out here taking liberties with human genetics, that ain't kosher lol
