I machine a LOT of carbon fibre plate parts, especially shock towers. I produce my screw holes by plunging with solid carbide 3.0mm flat slot drills. M3 screws will always measure up just under 3mm, a 3.00mm hole will be a clearance fit to the thread. If you produce them with a bigger cutter, you might have enough play to cause noticeable left/right imbalances on some car types, and make the car prone to tweaking on impact.
Some manufacturers interpolate round holes using cutters smaller than the final hole size. This is fine but in those situations you may well find the CAD designs show a larger hole than you actually end up with, as interpolating circles in this way can give more push-off or tool deflection, and some machines just aren't able to produce to size within that sort of tolerance.
The other thing I would add is that making these holes with steel drills is not a good idea, they will wear extremely quickly, giving you rough holes, undersize and not clean before burning up completely in a very short time.
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