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The equation that you want me to consider is the source of your confusion. The definition of the electric field, as other have already said, is (in one dimension ##r##) ##E=-\dfrac{dV}{dr}## not what you have. When you say E=-V/r, you equate the ratio of small differences to the ratio of the function ##V## to independent variable ##r## and then you wonder where the difference ##\Delta V## came from. When the field is uniform as between parallel capacitor plates, the ratio is constant whichmeans that the ratio of small differences is the same as the ratio of large differences in which case you can write ##E=-\dfrac{dV}{dr}=-\dfrac{\Delta V}{\Delta r}.##ZEROBRAINCAPACITANCE said:Well, when you consider the equation, E = -V/r, that too represents the strength of the electric field, but the - sign just indicates that the potential gradient increases in a direction opposite to the electric field.
Now here comes the tricky part. The denominator is a displacement and has magnitude and direction. The magnitude is the plate separation ##d##. Let's pick a direction from positive plate 1 to negative plate 2. Then the potential difference in the numerator is ##\Delta V=V_2-V_1## and this is a negative number because the negative plate is at a lower potential. Then ##E=-\dfrac{V_2-V_1}{d}## is a positive number which means that the E field points in the direction of the displacement that we chose. At this point we choose a symbol for the positive difference in the numerator whichever way the difference is taken, ##|V_2-V_1.## We call this positive difference "voltage" and we give it the same symbol ##V## as the potential function. It's not a very good choice but it is what it is. To avoid confusion we have to understand the context under which symbol ##V## is used because it can stand for two different things, the function ##V(r)## and the difference between two points in space at which this function is evaluated.
Your confusion stems from being unable to separate the two contexts when you see ##V## used in the same equation with different contexts. I don't blame you for this and I hope that you will get used to it after you have digested the duality of ##V##.
As I was typing this I noticed that @alan123hk posted and says essentially the same things.