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Dear Jon,
It doesn’t make sense to reduce the accuracy below 0.001, because 1 nm is the accuracy of the GDS file. So in the end, your extra points will be snapped on the 1 nm grid anyway. Although this minimum grid size can be reduced, that will also reduce the maximum total size of the mask and is not a common thing to do. If you want to do this anyway, have a look at my answer to https://nazca-design.org/forums/topic/opening-gds-file-regarding-its-precision-or-accuracy/
I don’t think your proposed solution of joining structures on different layers with different accuracies will work (but I’m open to being convinced otherwise…).
The upcoming release of Nazca does properly handle the integer overflow that you now see, which is caused by too many points in the polygon, as you already mentioned.
Xaveer