Manual and Remote Switches - 12VAC low-voltage landscape
Easiest question first - there's no issue underloading a power supply, so don't worry about that part of question 3.  

If there are three 12V taps on the power supply, would it make sense to power each of your three circuits (I'll just say circuits rather than zones as you call them) from each of the three taps?  

I don't think you really meant you'd run the return through the ground, that would be a bad idea... you want to run a two conductor wire through the circuit, and tap both conductors at each load so everything's in parallel.  

You can use wireless switches like the Lutron Caseta and Pico remote or similar products to do everything you want with respect to automation - it's come a lot way since your 90's X10 stuff.