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.