This sounds similar to how not all biofilms are cariogenic and can actually play a lot of beneficial roles. We have a lot of evidence[0] that in the past we had a much more commensal microbiome but the shift to a more cariogenic one was actually rather recent. I feel like it's very likely that our oral microbiomes simply haven't had enough time to adapt to the massive shift in modern lifestyles and diet but used to play a mostly beneficial role in our health, much like our gut microbiome did. I mean just look at Google Pics of the teeth of wild monkeys and apes. Pearly whites! No dentist needed

[0] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3996550/