I believe the best way to represent this table is as you have suggested: Using column 1 as a cell 5 heading and using three dots 5s to represent the blank entries.  In table A, the repeated headings should make things clear enough.

In table B, you could put a transcriber’s note as the column heading for the column that has no print heading: TNColumn 6TN.  This would provide some extra clarity.  Basically you would treat it as an embedded transcriber’s note.

Cindi