Hi Ross, I'd imagine the "empty.dgn" file units is probably just an oversight.
In regards to accuracy, I don't know why each seed has a different setting, however, the unit display accuracy is simply for readout purposes and does not directly affect 3D modeling or unification. For example, if two walls were .0118mm apart and you were to measure that distance, you would see:
.0 @ one decimal
.01 @ two decimals
.012 @ three decimals
and of course .0118 at four decimals
But as long as the unification tolerance was set to something greater than .0118mm, those two walls should still unify.