I do agree with you that individuals will be effected at even small levels of deficiency, even when we can't notice. However, culling those animals that are effected first is not covering up a problem - it's making sure that only those able to survive and thrive on the minimum pass their genes on. I'm not saying we should starve our animals and see which ones survive, but instead if you do have something like this come up where there's a possible deficiency to cull appropriately.
Just to clear things up a bit, I'm not saying you should ignore the fact that the toes are possibly caused by feed. In fact, I recommended the OP of the issue to add some rooster booster to make sure all the chicks are getting more vitamins. If I were them, I'd look at changing feed right away as well.
BUT... I would STILL not use that chick for breeding. Why? Because, if the other chicks in the brood are able to process the feed available, and he is not, he is not as efficiently processing his feed as the other chicks are. Meaning that even if their feed was perfectly acceptable, he would still, on maybe a very very small level, but still, not be processing that feed as efficiently (be it in terms of weight gain, eggs, chick viability, whatever) as the other chicks in that brood.
I'm not saying his toe issues are genetic or aren't genetic, but it really doesn't matter. Don't use that chick for breeding. Again, fix the feed issue, but don't breed that chick, really no matter how nice he is. He might make a good meat bird, but you don't want that feed efficiency issue passing on to other generations.