Steve, I am glad you brought this up. I wanted to say something similar. There are a LOT of different tortoise diseases out there and very few people are looking for them. There have been several papers published in the last 10 years or so looking at prevalence of disease in Turtles and Tortoises in Europe. One I read recently found something like 47% of the animals tested had at least one pathogen.Might as well wade into an argument, lol. Every tortoise baby (less than a year old) I have sent for necropsy - a total of 3 so far - has died of a disease or infection. And in each case, it was a different pathogen. I regret not sending others, because I don’t know why those particular hatchings died. I have observed “failure to thrive” cases in both tortoises I’ve bought and ones I have hatched. The ones I hatched were set up from birth using methods similar to what Tom recommends.
I strongly suspect that the rate of infections or diseases in such cases is being grossly underestimated. Most people don’t send them for necropsy to find out. Overall “hatchling failure” might be a catch-all for a variety of causes of death (husbandry or disease). Congenital issues are likely a minority of cases. In cases where congenital issues are common or a large number of hatchlings are just “weak”, I would consider a problem with the mother (e.g. disease or poor nutrition) or perhaps an egg incubation problem (e.g. too hot, or lacking temp fluctuation, etc).
It is too easy to say that a hatchling wasn't started right, or that it died from a "respiratory infection" or it was impacted. All that is BS without a necropsy and PCR work looking for the real reason.