Cheat!
I glue (zap-a-gap) the parts together, then from a NOT obvious angle, drill both parts at the same time.
Make sure that the pin length is less than the depth of the hole (countersunk). Put the pin in the hole followed by a drop of thin CA - it will wick the length of the pin and make the joint STRONG. Let cure.
Take a little putty (greenstuff, whitestuff, milliput, etc.) and fill the little bit of hole. Prime & paint.
If it is a large part and I am using a large diameter pin (use different pin diameters for different part weights) - I may do as above with a small drill, them enlarge the holes with the appropriate drill, leaving only a small hole to fill.
Clear as mud?