I really like those knobs! I always wanted to use something like that, but never did find a good place to do so. It does look like the doors are up to 1/16" inch off in height adjustment. But, if you correct that, the knobs will be that far off. But, if you try to re-drill the hole for a knob, it will probably be off in the other direction. But, if you then adjust the other knob, it may be off horizontally. Isn't cabinet making fun?
I put the knobs in the same spot on each door, so presumably straightening out any door errors will line the knobs up too. But (a) I think this is an optical illusion, (b) I'm not going to check if I'm right, and (c) if you think I'd try to fix it and thereby make it worse you're....well, probably right.