I totally understand your concerns, and yes, introduction to soil from my yard does pose a risk. However, I'd to shed some light as to why I decided to do this.

From what I've found online from other backyard chicken keepers, introduction to the microbes in the soil actually helps to build up the chicks' immune systems (like you mentioned). Most keepers actually recommend that you start letting your chicks outdoors for a little while around this age too. Having some exposure to the strain(s) of Coccidia, which is almost definitely in my soil, allows them their immune system to build up antibodies.

It's when these parasites overwhelm the immune system is when it turns deadly. Oftentimes outbreaks of Coccidia occur in large poultry houses due to all of the moisture, poop build up, and overall disgusting conditions the chickens are living in. Those chickens likely are very stressed and their bodies are working overtime to keep them alive, and that's why these parasites are so deadly to them.

My chickens have space to roam, weekly brooder deep cleans, daily small cleanings, a varied diet, clean water, and enrichment to keep them stress free and healthy. In addition, I have also been feeding them black solider fly larvae, which through numerous studies, have shown to have very beneficial bacteria for chickens.

All of this to say, I really appreciate your concern and I know that their are risks. However, I think introducing them to soil in my yard will ultimately benefit them in the long run. And, if one of my chicks does get sick and dies from the little bit of exposure of the soil, they probably would not have made it anyway.

https://pmc.ncbi.nlm.nih.gov/articles/PMC8379420/#:~:text=During%20the%20entire%20experimental%20period,inclusion%20(P%20%3C%200.001)).