I think the issue is more that that was the best opportunity to exposit the core's ability to produce bioweapons to defend itself and shoehorn in Lao's sacrifice play (which doesn't make a ton of sense anyway because he should have been in custody and not sneaking in the non-existent back door of the Lifehold with a thoroughly-impractical lance). The former, I expect will come up later as part of some manner of conspiracy around the ECP (even if the chimeras weren't the intended product, giving the computer responsible for mankind's resurrection the ability to generate bioweapons to protect itself is not exactly a normal idea employed by honest people that aren't tinkering with the fabric of life itself), similar to J-bodies, the latter, I'm not sure. I don't really know how else that could have been made to work, since if it was collateral damage during the fight with the Vita that wouldn't result in a distinct boss fight against the chimeras or give a chance to explain how the whole thing worked, and wouldn't get Lao in.
Does that make it good? Not really. But consumers of anime and JRPGs tend to be a little more willing to accept monologuing while the Big Bad punches the Ultimate Mcguffin of Destiny, so I can see why they felt it was good enough and I just kind of rolled with it (particularly where the same result could have been achieved by having Luxaar get one good hit in that scrambled things and triggered the defense mechanism, so it's not like the actual plot-relevant details really changed for the dumb trope). In the grand scheme of dubious plot decisions in X, that's pretty minor.
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