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.

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356804/