A friend did something similar, but not nm-scale (just for decorative purposes). You kind of need a patterned surface for tracking though.
...and measure timing between each one (average over many revs) before start to get phase offsets for each to feed into PLL?
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Depends on whether you need dimensional accuracy or just track-to-track repeatability I guess. That sounds like it'd work for the latter.
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I think it would work for either, no? Once you correct for phases of minor marks, everything is stable relative to the primary one.
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I think the issue is you can't easily correct for the spindle not being perfectly centered and the like. That'll introduce consistent error.
End of conversation
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