I had to print something with a hole that had a "flat part" to it (like a D-shape), of 12.5mm diameter. I just printed a test piece, measured it out, and then as mentioned, just "fudged" the radius. Came out just about perfect.

For 3D printing just about any precision part, there is often some trial and error to get the diameters right (often depending on your printer as well as slicer settings), and you usually get the best fit if you can drill or file things a bit.