With the Joggy Thing running in LinuxCNC 2.7, touching XY off on the fixture was trivially easy:
The pips are 100 mm apart at (-50,-50) and (+50,50). Astonishingly, the laser aligner batteries are in fine shape.
I should have protected the platter before drilling all those holes:
All’s well that ends well:
It looks even better in the dark, although you’d never know it from this picture:
I wish I could engrave those patterns on already-drilled platters, but dragging a diamond point into a hole can’t possibly end well. I could deploy the Tiny Sandblaster with a vinyl mask, if I had enough artistic eptitude to lay out a good-looking mask.
The Smell of Molten Projects in the Morning 
I’m curious, does the pattern end up with any “depth” or 3D-ish appearance to it?
The pressure produced barely a scratch: it’s visible and feel-able, with no depth worth mentioning.
Any side force on those springy bars deflects the point: it needs a less bendy holder!
Dragging it into a hole is probably fine.. it’s dragging it back out that’s going to hurt. :) I bet you could modify the g-code generator to interrupt the cuts around the known hole locations…
I actually started tweaking the gcmc code to include a list of keep-out circles. A few dozen lines of code later, I realized I’d have to figure out whether each move intersected each circle, compute the intersection(s), then insert lift and drop moves. Shortly thereafter, I checked my stack of defunct hard drives and common sense broke out.
Why not make plugs and press them into holes for the engraving process? Few thou difference shouldn’t be a big deal, it’s just big drops you have to avoid
I deburr the holes, which puts an irregular conical depression around every one. I’m sure a careful epoxy fill would work, but … Contemplating. Junk. Drives.