Here's our experience, FWIW. My eldest child has no apparent midline or other defects (except for a somewhat high palate), but she has a lot of digestive issues. Her infancy was a nightmare of colic, food journals, etc. She's never had normal digestion (even with probiotics, strict elimination diets, etc), is a very picky eater, is prone to stomachaches, and has frequent tantrums. She's currently off gluten, all food additives, and high-salicylate foods. It's helping, but not enough.
Child #2 has a high arched palate and a slightly asymmetric "crease," but no sacral dimples. As a baby, he had frequent vomiting and stridor (dx as laryngomalacia), which got much better when I cut out dairy. As a preschooler, he dislikes cheese and other sour milk products, but drinks milk with no obvious effects. His behavior is easy-going, his stools are pretty normal, and he's not very picky about food. He does get a little loopy from high salicylates and food dyes, but nothing dire... e.g., I might let him have a little at a party, whereas with DD1, that would be a disaster.
Child #3, my toddler DD, was born with several congenital anomalies, including a serious heart defect. Her laundry list of "red flags" includes deep sacral dimples and an odd-shaped crease. She also has a tongue tie, as do I (it runs in my family, though AFAIK none of the other stuff does). Oddly enough, though, she doesn't have a high-arched palate, nor does she have any apparent digestive problems. This is despite being mostly bottle fed for the first several weeks, and getting formula supplements and tons of abx while in hospital. She's also the "easiest" of my children behavior-wise, and her social and verbal skills are considerably advanced for her age.
At a superficial glance, it would seem that my kids are getting less healthy in terms of midline defects, but more healthy in terms of digestion and behavior. I don't know what to make of that, though.
We've been told that it's likely that DD2 has a one-off genetic disorder, but really they have no clue. They just know that she's doing much better than anyone could have predicted, given how bad things look on paper. I suspect that good nutrition has been a huge part of that.
(BTW, our diet is based on nutrient-dense traditional dishes, with mostly organic ingredients, and very little in the way of processed food. I've been eating this way since before I met DH, so I'm inclined to doubt that a "deficient diet," per se, was the cause of my children's problems. OTOH, an excess of poorly tolerated foods, and resultant problems with digestion and assimilation, could well be part of the picture. I'm hoping that the SCD will help us all with this.)
As for me... I have a lot of food and environmental sensitivities (out of all my children, I'd be most similar to DD1), but nothing strange in the way of dimples or creases. As mentioned, I was born with a tongue tie, but it was clipped very soon after birth. I wasn't breastfed, but it was bad enough even to interfere with bottle feeding. My palate seems moderately high, and I've had to have orthodontic work.
Sorry if I've messed up the theory with my anomalous data points
, but I guess life is complicated that way!