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That would be a better solution. I found drilling through the hard plastic sole "above" the main rubber sole to be a real pain. It would melt something rotten and clog up my drill. For some of the stud holes I had to drill into the plastic a bit because the rubber was worn too thin to accept the full nut. Another pain with a flanged solution would be that I'd probably want to countersink the inner sole to account for the flange and that's tricky to achieve.
In the end, buying proper CX shoes looks like a much better option.
fizzy.bleach-
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!
Raphael
How about using something with a flange and fitting it from inside the shoe so that the flange sits directly underneath the insole. A Tee- nut without the prongs would do the job.