2 sided cut, not carving

Easel Pro, on a XCP.

I mentioned this need on another post, but thot it best to start its own post on this subject.

I have a 3" long end mill (OVL).
I have a 4" chunk of wood, I’d like to cut circles out of.
I’d like to cut 2" deep, from both sides, in 1/8" or 1/4" increments.

How would you flip a chunk of wood, and still get perfect alignment to complete the circle from the other side?

I would drill 1/4 holes on the centerline of the board on each end. Then I would drill two holes in my waste board to accept 1/4" pins or dowels the same distance apart. Theoretically one should be able to flip the board over and re align it with the pins. This assumes perfect alignment, accuracy, and repeatability. In reality, I bet the wheels would still need some tweaking.

Or…
I’m thinking I could have the XCP cut a square around the circle, such that the circle is in the middle. Have the XCP cut the square out. Now, I have a square, with a circle dead center…yes? Flip it, clamp it, and go.

Or am I confused?

That could work too.