I would expect the output from Make2D on Clipped geometry to be as what is shown in the viewport - that the clipped objects are capped and that features that are hidden by this cap are put on the hidden layer of Make2D. In these images you can see that that is not always the case:
The arrows point to lines that should be hidden. (and I guess there also should be a hidden line on the left side in the box object)
A second issue with Make2D of clipped objects is that I expect the curves that are put on the
ClippingPlaneIntersections layer and that are the result of clipping closed objects to be joined and closed curves. The clipping plane intersection of the box object are several line segments that can be joined into a closed curve (and should be the default output if you ask me) but the clipping plane intersection of the spring object are curves that cannot even be joined into a closed curve.
The red circle in the image above is enlarged here:
make2D Test - model.3dm (933.2 KB)