Your intuition that cutting along these curves should not result in different surfaces is completely correct. The following two pairs of curves, $(\alpha,\beta)$ and $(a,b)$, cannot be sent to one another by any homeomorphism, for the connected components they cut off of the surface are not homeomorphic.
> ![Curves](
However, this is somewhat of a special case, as I chose a _bounding_ pair of curves that have different genus. Note that the Primer mentions that the given statement of the change of coordinates principle is "rough." Pages 39-40 give examples of different types of pairs of curves, and mentions a few where only the intersection number is needed, e.g. when it is equal to one.