Hi Nate,
If you are setting the machine origin to the top of the canvas, and zeroing out your machine's origin to the top of a workpiece, the tool should never travel higher than the Safe Z rapid height from the top of the workpiece. The only thing that would make it travel higher than the Safe Z height from the top of the workpiece is if the machine is actually being zeroed out below the top surface of the workpiece. Where you see the toolpaths relative to where you set the canvas origin is where they will be relative to where your machine is zeroed out. There's also the possibility that some kind of work offset is being applied by your controller and needs to be cleared/zeroed but you'll need to figure out what those may be for your specific machine.
Don't forget to re-generate operations' toolpaths after making any changes to the canvas origin! That can cause some unexpected placement of cuts if they're not generated for where the machine origin is currently set to. This is something we're looking to change soon as a number of people have found the need to adjust where the machine origin is after creating operations and generating toolpaths but where the machine origin is placed relative to the canvas is "baked" into toolpaths when they're generated - which isn't necessary and we should only be applying the origin when exporting G-code instead.
Keep me posted!
- Charlie