Hi Doug,
You can offset lower where the medial-axis carving operation will cut with the Depth Offset parameter that shows under the Medial-Axis Carving Operations toward the bottom of the operation parameters. A positive value will offset downward, where zero represents the top of the canvas, so you might have to calculate what offset to use. When your mouse is in the 3D view you can put the cursor on the point of the canvas you want to get the Z coordinate of by looking at the coordinate readout on the status bar at the bottom of the PixelCNC window. Just subtract that value from whatever the Z coordinate is for the top-plane of the canvas. If your machine origin is set to the top of your canvas then you just use that number, except flipped positive (because all coordinates on the canvas surface, with the origin set to the top-plane of the canvas, will be less than zero). That will put your medial-axis carving cutpaths where you want them! Rapids will stay at the Rapid Height above the top of the canvas though, regardless of your Depth Offset.
Just as an FYI you can also composite your text onto your canvas subtractively to get a better visual representation of what you're trying to do. For actually generating cutpaths I would do like you already are and trace the text to paths to use as contour input for the operation, or just have the layer groups with each text-layer inverted and Z-Fill set to the top of the canvas, which seems a bit more roundabout though but it will do the same thing.
- Charlie