I know that it is more expensive / harder to find a car with an automatic transmission to rent, but why is that the case?
My first guess would be that autos are more expensive to buy, and that any excess wear and tear on the car caused by people who are bad at driving manuals simply doesn't come close to the increased purchase price.
Another option would be that people prefer to drive manuals, I guess?
This answer states that they used to have better fuel economy: What is the most common transmission type for rental cars in Japan? Is that still the reason for primarily offering manuals?
The above question & answers indicate that Japan is now mostly (exclusively?) automatics in the rental market. I believe the same is true of NZ and Australia. Are those countries ahead of the curve, or are European countries behind it?
EDIT: Of course, NZ and AU import a huge number of their cars from Japan, so that's probably trickled on through to the rental market (Japan produces less manual cars, countries can't import as many manuals, less available to buy, rental companies wind up with mostly automatics).