Wow, that definitely is odd. This also happens in V5, so it's not a phenomenon related to the WIP. If you Explode your unioned object, then _RebuildEdges, you will see that the faces where the isocurves are "broken", the edges pull away and actually become arcs!
This may be a combination of the fact that your objects are pretty small w/respect to the tolerance and the faces concerned are not trimmed rectangular planes, but non-rectangular planar surfaces. But it still should work correctly IMO, this looks like a bug to me... @pascal
If I replace the trapezoidal sides with trimmed planes, the problem disappears...