It lives in a very specific part of your intestines where other microbiota keep its growth in check and under control. Other places, like the small intestine, don't have that protection. If your large intestine gets perforated and the bacteria can escape directly into your bloodstream, you can develop sepsis and die pretty quickly.

Not a food scientist, but the explanation I've heard is that some bacteria produce toxins as metabolic byproducts that aren't destroyed by cooking. You can have a hamburger that had a colony of E. coli living in it that's cooked well done and become sick from the toxins left behind.

Also, undercooking can leave some bacteria alive. If a piece of meat has a small amount of bacteria right before cooking, this will probably be fine. If it was heavily contaminated at the source and packed with bacteria by the time it's cooked, 10% remaining of a huge amount is enough to colonize you and make you sick.