It's because a power supply is grounded via the mains, as is your amp, and the negative of the power supply is (normally) connected to the mains ground, therefore the negative has to be the ground. With a battery, neither positive or negative is connected to ground so you can connect the positive to ground which effectively makes the negative 9v less than ground i,e -9v.
Sorry to disagree. Adapter outputs are not grounded. They float just like a battery. There is no DC pathway between the mains and the adapter output except via the amplifier.
wiring a power supply the other way around simply doesnt work.
It's not clear to me what you mean. Are you trying to convert an existing positive ground circuit to negative ground by reversing the adapter connections? That won't work. Do you have a negative center pedal and a positive center adapter? Reversing the connections will work.
In general, 'center negative/positive' and 'negative/positive ground' are separate issues, and have to be addressed independently. You can have a negative or positive center on any single-rail pedal, positive ground or negative. You just have to design it appropriately. Negative center is just a convention, it has no impact on the electronic operation of the circuit.
Negative vs. positive ground, on the other hand, is built into the topology of the circuit. If you want to change it, you have to redesign the circuit.