First, observe that
$$\sum_{k=0}^{\min(p,q)} \begin{pmatrix} n \\ k \end{pmatrix} \begin{pmatrix} n - k \\ p - k \end{pmatrix} \begin{pmatrix} n - p \\ q - k \end{pmatrix}
= \sum_{k=0}^{\min(p,q)} \begin{pmatrix} n \\ k \end{pmatrix} \begin{pmatrix} n - k \\ p - k \end{pmatrix} \begin{pmatrix} n - k - (p - k) \\ q - k \end{pmatrix}$$
This means that there is a clear pattern. You could imagine that you have $n$ labeled balls in a box and three buckets: A, B, and C. You take $k$ balls and put them into bucket A. There are $\begin{pmatrix} n \\ k \end{pmatrix}$ ways to do this. Then you take $p - k$ balls from the box and put them in Bucket B. There are $\begin{pmatrix} n - k \\ p - k \end{pmatrix}$ ways to do this. Lastly, you take $q - k$ balls from the box and put them in Bucket C. There are $\begin{pmatrix} n - k - (p - k) \\ q - k \end{pmatrix}$ ways to do this.
The total number of ways to execute this procedure is given by the sum on the left-hand side.
Now let's consider a different procedure. Suppose all balls are back in the box and we have stickers with the labels "B" and "C". We choose $p$ balls and label them with the sticker "B". There are $\begin{pmatrix} n \\ p \end{pmatrix}$ ways to do this. Now we choose $q$ balls and label them with the sticker "C". Note that a ball can possibly have two stickers on it, "B" and "C"! There are $\begin{pmatrix} n \\ q \end{pmatrix}$ ways to do this. The total number of ways to apply these stickers is equal to the right-hand side of the equation.
To see that the two values are equal, we now put all the balls with only sticker "B" in bucket B and all the balls with only sticker C in bucket C. We are left with a number of balls that have both stickers, "B" and "C". We put these balls in bucket A. Suppose that $k$ balls ended up in bucket A. Then there are $p - k$ balls in bucket B and $q - k$ balls in bucket C. We see that there is a one-to-one correspondence between the ways of putting the balls into the buckets A, B, and C, and the ways of applying the stickers "B" and "C" to the balls.
As to your diagram, consider drawing a third disjoint blob in the diagram on the right in purple color. Then on the left-hand side, you can create a third region which is the intersection between red and blue, thereby obtaining three disjoint regions.