You're not missing anything except that your bores are worn. Measure the gap at the top of the bore, just below any ridge, and then measure again near the bottom of the bore; bet you'll find quite a difference and that is bore taper; it can be quite different for each bore so you need to check them all. If any of the bores are tapered, you need to fit any file-to-fit rings at the bottom of their stroke (about 4" down in the bore) and then live with the gap near the top; if you fit them at the top, then they close up and can seize in the bore near the bottom of the stroke when things get hot.
Know that tapered bores 'work' the rings and they won't last as long and don't tend to seal well. I've done a few hone-only jobs in the past when I was young and poor, with tapered and out-of-round bores, and the worn cylinders never operated nearly as well as the others, and those engine clearly had extra blowby . The ring grooves were corrected with rings spacers so the rings were held flat, but the worn bore issues could not be fixed by just new rings alone.
