The strong and flexible material from Shapeways has a somewhat gritty finish (like sandpaper). When polished, it becomes much smoother, but you lose a little bit of material. The basic resolution of the printer affects what tolerance you need between parts. Shapeways provides this specification for their strong and flexible material: ± 0.15 mm, then ± 0.15 % of longest axis. If you think in terms of plotting pixels that are 0.15mm each, you can see why the exact result is somewhat hit or miss:
In the layout above, the blue area is where a nominal square might fall in the worst case. It may include the blue pixels or it may not (using the green), depending upon where your edges fall in the print job. In your squared-the-circle example, if the square was 10mm x 10mm, the inside part should be 10mm - 0.15mm = 9.85mm and the hole should be 10mm + 0.15mm = 10.15mm. Best case you get a snug fit, worst case you get 0.30mm of slop (abuut a 0.0059" gap all around).
On the other hand, their SLA printer has a resolution of: ± 0.025 - 0.05 mm for every 25.40 mm. This means your 10mm parts can be 10.025mm and 9.975mm respectively. The 0.05mm specification is the shrink due to curing the material and is applied to both parts. To be more accurate, you should add an additional amount to your part by 0.05/25.4 or 0.001968 * 10.025mm (in this material) to get 10.045mm and 9.995mm respectively.
If you’re making this for yourself and don’t mind some sanding and fitting, just use the actual dimensions and it will either be snug or too tight (BTW, sanding nylon is not especially easy). Or offset everything by 0.075mm and use epoxy instead of superglue
[EDIT - I changed the picture to indicate 0.30mm pixels instead of 0.075mm or 0.15mm]