These incidents are relatively rare in consumer devices (so exempting RC lipos and cheap knockoff products with no protection).
Temperature monitoring has become very common. The primary heat source is almost always the LED, not the battery, but it would be sufficient to detect a battery nearing thermal runaway. Low-voltage protection is common, but sometimes only a warning blink rather than a hard cutoff based on the idea that leaving the user in the dark might be worse than damaging a battery.
Some models have onboard charging, most often through MicroUSB. Correctly charging a single Li-ion cell is not difficult, and I haven't seen one get it seriously wrong yet.
LiFePO4 has seen a little use, but is not popular due to its much lower energy density. I suspect this has kept it out of other portable devices as well since users always seem to want longer runtime in ever smaller devices.