Choosing quick-disked raw materials strategically might be marginally worth it- possible puzzle for the analysis types.
I made an Undine in a recent game whose stats were absolutely hosed (relative to base stats- I know they don't look impressive anyway), despite the parents being high-end critters. Neither had the right stat pattern for an Undine, although they did match up well to each other. I hadn't thought it would matter for an item-bred creature, or that even with the wrong pattern 999s on the parents could become -50s on the baby.
So, I looked up the patterns and disked up some critters with the same stat pattern as an Undine. Got myself a straight-stats Undine, which was better, but I wondered why I didn't get bonuses, at least small ones, for the match.
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To explore this, in this run-through I made my Ghost and Ducken from straight-from-disk monsters with specific stat patterns.
So, only 8 points overall, but I think the difference is mildly interesting; the match that was perfect all through got me base stats. Just grabbing a couple of Mocchis or Zuums from the Market gets me base stats. But the one that went from almost to a perfect match got me bonuses.
I think the game specifically decides to account for or ignore the parentage depending on something, just automatically giving you base stats if you do certain things that indicate you are just blundering along, and applying the rules when you seem to be putting some effort into it. I have, of course, only this sort of evidence for that conclusion.
I do find it interesting that the perfect match didn't do anything but the match that came together altered things, though. Just an observation.