Changing frame of reference is making me more confused. Can you provide me some graph with potential energy set to zero. Or can you please elaborate on it.
It is exactly the same concept as temperature scale or elevation. When we say that the elevation of Mt Everest is 29,000 feet, that number doesn't mean anything by itself. What we mean is that the elevation is 29,000 feet
above sea level. Sea level is given a value of zero. It is a frame of reference. Just so, the Dead Aea has an elevation of -1400 feet or thereabouts relative to the frame of reference (sea level).
You could use anything as a frame of reference, but the optimum choice may change from situation to situation. When you say how tall you are, your frame of reference is the ground directly under your feet, which you set to zero intuitively. My height is roughly six feet above the ground. I live in Chicago which has an elevation of 600 feet above seal level. I could easily say my height is 606 feet above sea level, using sea level as a frame of reference for my height instead of the ground under my feet. But it would get really confusing to compare the height of people who live in different places if they all used sea level as their frame of reference. So we choose sea level as a frame of reference for geography and the local ground as a frame of reference for our personal heights. Now, you could just as well use the Dead Sea as the frame of reference for geography. In that case, Mt Everest would have an elevation of 30,400 feet (29,000 ft above sea level, which itself is 1400 feet above the Dead Sea - 29,000 + 1400 = 30,400). Choosing a different frame of reference does not alter the
differences in elevation between any two places, as long as all the elevations are expressed relative to the same frame of reference.
In your example, your frame of reference (your sea level) is two completely separated atoms, which we set to zero potential energy (O kJ/mol). The bottom of the well (the dead sea) is therefore some negative number (call it -X kJ/mol). The bond dissociation energy is the difference in energy between the energy of the two separated atoms and the bottom of the well, or X kJ/mol (0-(-X)=X). But we could call the bottom of the well zero kJ/mol, in which case the potential energy of the two separated atoms would be +X (just as the elevation of sea level would be +1400 feet if we called the dead sea 0 feet in elevation). Reassigning the bottom of the well does not change the bond dissociation energy, which is just the difference between the two points on the y-axis. It's still equal to X kJ/mol.
As you can imagine, there are some reasons why we usually assign the lone atoms to be zero rather than the bottom of the well. Maybe you can think of what those reasons might be.
Make sense?