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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.
In case anyone's interested, those home drilled studs all utterly failed within a couple of light CX training sessions. The rubber is just too soft a substrate.