Yes, you can program using XYZ like in a mill if your Y travel allows it. You don't have nearly as much as you do on a mill, but then you can use the C-axis to overcome some of that. You really only need to use Y if you're doing work that's off center. If your bolt pattern is radial then you just position once with X and Z and use C to drill a hole at every rotation.
We have an MX2100 I've just finished fixing up a post for so let me know if you have code specific questions. The biggest thing I ran into jumping into the millturn world was all the interlocks and codes to switch between milling and turning. They can pile up and get confusing if you're not used to them.