Family values

The explanation for why we used 9,9 as the initial x / y values for the Square is a little bit twisty, but here goes:

If we hadn't first set that initial x and y values of Square to 9,9 (say, for example, if the initial values of Square were 0,0), then any Square that had an x value of 0 or a y value of 0 would not be overridden. You wouldn't have seen the value turn bold in the Inspector panel. Non-overridden values are not "protected"—they're at risk of being modified whenever a change from another instance is applied to the Prefab.

Imagine yourself making the above changes to the bottom-right Square, which has its x and y values set to 2,2. Once you click on Apply, x:2 y:2 become the default values for all squares whose values were not overridden. That means that any Square matching the initial default values of x:0 or y:0 would have those values replaced with x:2 or y:2. The top-middle square, with its overridden value of X:1 and its default value of Y:0, would see its unprotected...