St. Thomas, as has been pointed out, was wrong about the biological facts in many cases, and thus iffy on the theological conclusions he may have drawn from them. Humans creating a chimeric zygote was undoubtedly not even on his radar.
The points made in Humani generis seem to have been primarily intended to safeguard the universality of original sin rather than to specifically deny either polygenism or the possibility of humans arising by other than natural generation. That’s why the “We can’t see how this would be possible” language is used. Presumably, if in a later generation theologians come up with an explanation that puts original sin in all the right places but allows for those possibilities, the Church could declare such thinking acceptable.
More specifically, the concern at the time seems to have been with an alternative notion of original sin that has it arising from mere imitation of our sinful forebears, rather than as an integral part of fallen human nature. As long as it is maintained that we are ontologically deprived because of the acts of our first ancestors, I don’t think the Church would have a problem with other notions than that of original sin being literally transmitted through sex (or meiosis). Indeed, I don’t think that’s been the official line for some time, as it leads too easily to the pseudo-Augustinian “sex bad” attitude.
As an earlier poster pointed out, the current conception of original sin emphasizes more the loss of supernatural gifts than the acquisition of some kind of “stain.” Those gifts aren’t part of human nature unless God chooses to grant them, so the lack is “transmitted by generation” in the sense that our parents have no power to give us the extra God-stuff. That would remain true of any mortal human-makers, by whatever process.
As to whether a chimeric individual would have an animal or human soul, that again depends on God, and we have no way to know unless such a being develops to the point where it can start acting recognizably human (or failing to do so). Despite the worries of some, I’m pretty sure Catholic teaching doesn’t allow for “stealth” soulless folks who act just like people but aren’t really, so if they act just like anyone else, God has granted them souls.
Since producing chimeric children (and eventual adults) is not the goal of the program, we should not see any such thing from these scientists, at least. In the current, barely developed form, should the zygotes be treated as human or animal? That’s a good question, though if “nuclear material human, 1% cow” is true, I’d vote “human” for the current bunch. It seems the Church does too, or at least would sooner decry some animal experiments than take a chance on approving the slaughter of humans.
Usagi