Was your drill bit blunt? Does the sole have kevlar or something in it?
I bet you'll barely be able to feel a flange through insoles and socks. I just google imaged cx studs and it looks like they're placed right at the toe and mid section of the shoe, ie away from not the balls of your feet where the pressure is when running. I also saw some blade designs that look like front teeth and some that looked narrower and cylindrical rather than the conical football stud shape I'm familiar with.
A thermal bridge?! Maybe you could get stainless tee nuts if you're worried about that!