The straight answer to your question of how plans A and B were supposed to work together is simply that they never were.
As you already said in your other question, officially plan B was just a fallback for plan A in case that didn't succeed. But even more so inofficially plan A was never expected to succeed at all. So no, the creators of the plans have most probably not thought about the political and philosophical implications of mixing artificially born natives and naturally born colonists into a single society, not that such considerations would have been of a particularly high priority anyway.
But I'm afraid this also is all there is to answer here. If your further question is how this new society would pan out given that it has to now, this is beyond the point of the film's story, the information available to us, and thus the site's scope. We can't really speculate about how any government or society on this new colony would work, let alone the broader philosophical considerations of this issue.
But yes, colonizing a new world and/or large-scale artificial breeding of humans most certainly poses a lot of problems, none of which either the film or its characters concerned themselves with, though.