So there are lots of companies which already produce metal plates with this hole punch design, but I'm not sure if I've seen one without the template etched on to the metal.
You can easily reduce the size of the plate and/or increase the size of each box by overlaying words 13-24 on top of words 1-12. For example, one dot in a box for words 1-12, two dots for words 13-24, or three dots if the letters overlap. Or a vertical line, horizontal line, and a cross. Or any other such arrangement. Or even do the same with 1-6 overlaid with 7-12, since 12 word seeds are perfectly adequate.
Excellent suggestions in theory, but a hammer and a punch aren't the most precise implements, and from experience I can tell you that attempting to punch centering holes in close proximity to one another is nearly impossible without making a mess of things. Especially if you're starting with a small substrate,
like one's I used for my seeds.