And for millennia people died from contaminated food even when it was fermented. Fermenting isn't a perfect 'kill anything possibly toxic' preservation mechanism[1], and even non-toxic contamination of fermented foods can make it taste awful/inedible. Given 'modern microbiology and food hygiene practices', why would you not mitigate getting things you know are possibly an issue (like shit) into your food.
That tells me the microbial colonies are resilient to any harmful pathogens introduced by getting your dirty hands involved. Isn’t that precisely the point?