I think the rivet you have a picture of must be from superstructure above 'E' deck. If you look here: http://curiosity.discovery.com/topic/we ... ures33.htm
at images 35 to 37 you get a good idea of how it was.
When they punched a hole in the steel, it left a bigger hole on the side away from the punch tool. That's why the hole was not parallel sided. It also left a ragged edge round the rim which had to be removed. It was removed by a 'Rimer'
They really did have problems with holes not matching. These were called 'unfair' holes. They solved the problem with special tools. One was a 'drift punch' a tapered steel tool not unlike an old carving knife sharpener which was driven through both sets of holes in an attempt to align them. There were two Rimer tools. Both were steel tools much like the previously described Drift Punch. One had four parallel grooves which formed four sharp edges 90 degrees apart. End-on, it looked like a cross. The other was much like a flat bladed rasp file. These were also used in trying to 'fair' 'unfair' holes.