This is probably because I learned to sew with the Honeyboy pattern (sewing on the lines)... but in any case.. When I've made two-layer Turned and Topstitched PUL covers (PUL shiny side inside, cute fabric out), this is what I do... Trace the pattern, cut out the fabric an inch outside of the lines, and use that inch for pinning. Once the layers are sewn together, most of that inch gets trimmed off (except the bits the elastic is sewn to), so no worries about pin holes there. I'm assuming this is not how most folks sew, but it usually works well for me.