The "Thermal Shutdown" of the CPU is 100C (212F... water boiling point). That is... The CPU will throttle itself down below 600MHz until the temp drops to an acceptable range. Yes, you can get the CPU to 100C and keep it there without damaging it. And allowing the CPU to hit this temp is not a design flaw. The notebook is designed to take that heat.
Now, if you choose to run an app that is either poorly written, or designed to run both cores at 100%, that is your choice. When you do this, I would recommend taking action to prevent damages.... to yourself.
The documentation does in fact warn you that these temps are possible.