If you have two position pins in a straigt vertical or horisontal line, then you just flip the board. The CAD program will not care if the two pins are a bit away from the center of the board. So in theory, the two holes could be top-left and bottom-left and after you flip board they are top-right/bottom-right. Just that the CAD program produces data relative to the holes so the machine in that case on one pass do most work to the right of the pins, and after flip have most work to do to the left of the pins.

The issue is that you need to align the pins so that you can flip the board while maintaining exact relative position. With two pins in diagonal corners, you can't flip the board because the board must then have four holes - it will be the two opposite diagonal holes that would be used after board is flipped. No such issue with the two holes in vertical or horisontal line on board.

+--------------------+
|                    |
|                    |
| o                o | <= not symmetrically placed
|                    |
+--------------------+

+--------------------+
|                    |
| o                o | <= but still ok after flip
|                    |
|                    |
+--------------------+

So as you see from above - having the holes symmetrically just means that you can make maximum size PCB in relation to table size of machine. As long as board is smaller, it doesn't matter if you have an assymetry. Just that by minimizing the longest distance from hole to side of board, you get board better held down.

One interesting thing with very narrow traces is that the bit can "push" the trace sideways, if bit isn't sharp enough and movement speed suitable.