Boiling contaminated water is much safer than not doing so, as it does kill parasites and bacteria, but not all. And contaminants such as heavy metals, pharmaceuticals, pesticides, some poisons, and insecticides, are not removed through boiling water.
Anything producing meat has to drink water, so the same applies as above.
Grouping it all into "dysentery" could just be an easy way to have a catch all name instead of wasting time coming up with a name for every ailment.
It does feel like the percentage chance of getting dysentery is higher than the listed percentage to me also. But I'm not really convinced it's not confirmation bias on my part as I don't tend to count how many times I eat verses how many times I've become sick.