We have been through this before, what CAM system are you using, 3D clearance routines can use flat 1/4" cutters, finishing profiles in most cases use ball or bull end cutters. If you use flat cutters the lead and trailing edges of the tool dig into the work surface.
If the tool is digging into the surface then the CAM is allowing for the radius of the tool to put the contact point in the correct place.
Mach has no setting that can alter this.
A straight line in X & Z will be working from the centre line of the cutter so will overlap the edge of the cut path by the radius.
I have been able to reproduce this with two different CAM converters, Vcarve Pro and MeshCAM, and two different 3D designs. Vcarve does not show the clipping in its simulation nor does the GCode machine simulator for MeshCAM. Always the same thing on the machine; on any 2 Axis move involving a Z movement toward the top of the table (X-Z or Y-Z), the surface of the material along the axis gets clipped when the Z is plunging to the new position. What you are saying is what I have suspected from the beginning.
I specifically asked both software vendors if by default the CAM conversion for 3D roughing or parallel finishing assumes a Ball Nose tool, even though both software programs allow you to select any tool. Both say no.
The attached picture is of a part machined full thickness (3/4") PTFE, a circle slot with a ellipse island in the center. No top of material machining at all.