Hello Hogan;
I've worked on projects where any bolt hole punched through material thicker than 1/2 inch was to be punched or drilled undersized and then reamed. I just took a look at my copy of the New York Steel Construction Manual in which they require bolt holes in primary members to be reamed. So the project I had in mind was most likely a NY bridge job.
As for plug welds and slot weld per D1.1; clause 5.15.3 Material Trimming - it says any sheared edge that will carry a calculated stress and is subject to cyclic stresses has to be trimmed. There is no statement limiting the requirement to butt joins, fillet welds, etc., so I would believe that it applies to punched holes as well as sheared edges since the punch utilizes a shearing force. Maybe someone else can point us in another direction that exempts punched holes for plug welds.
Best regards - Al