I've run into this issue, but for different reasons: designing microfluidic networks at the micron scale using mm sized page sizes. I ran into the resolution limit of inkscape here--rounding and point placement quantisation to whatever inkscape uses internally as its fundamental unit.
It would certainly be nice if one could specify the native unit system and required precision, e.g. µm, nm, mil (1/1000"), 1/16" etc. to n d.p. to be able to work with suitable precision and accuracy for the task at hand.