Dui, ni shuo de dui
I think the main difficulty here is to make sure the holes will be 100% parallel to your extrusion.
For this, I suggest you to use the probe functions of Estlcam, there is a nice feature which allows you to check for alignment and automatically compensate via software. Just use a long alignment probing distance, to make this as accurate as possible.
This way, you can make sure that everything is aligned very easily.
Also, I don’t suggest you to make deep holes, just mark the spots by drilling one or two millimeters with a tiny bit, then use a drill press. There is a good chance to screw up if you try to drill through the whole thing with the MPCNC.