I have found that there is aways going to be some misalignment with the Shapeoko no matter how careful. I use the Carbide 3D Touch Probe and a threaded table. I use Fusion 360 and Carbide Motion.
Two problems I’ve encountered are.
When using a 2-flute end mill the origin may be off due to the rotation of the tool during the probing.
You can be tricked up if the actual stock is not exactly the same as the stock in the CAM file. Always check this.
When I need to be very accurate, I make a test cut with a duplicate tool path, but input enough “stock to leave” to allow for resetting the XYZ axis if necessary. I then check the dimensions of the test cut with callipers against the stock dimensions. For example (if the cut is centred in the stock). Check if the hole edges are equal to the edges, if so then things are aligned. If the front side of the hole to front edge is .040 thicker than the back side of the hole to back edge, then I move the Y axis by 0.020 and zero it. Same thing for X and Z if necessary.