rmcelling, you don't need any additional tool or terminal to tweak applications and desktop. there is configuration editor for setting and changing configuration (in different versions of mate the configuration tools are also different and their structures are different too).
if you consider point 2 the most important sections of configuration editor are apps and desktop '> mate. this is a bit like registry editor for windows. but here is simpler. it's smaller and there are some hints at the bottom. moreover there is procedure to go back - look at list recent keys (ctrl+R) reference/option. some settings might be done by preferences in different places of the system. so sometimes there is no unique way to solve the problem.
about point 3. remember it's beta version (Peter is waiting for mate 1.8 to finish it). do not suggest it for newbies. I use it because of hardware problems with my notebook but prefer point 2 (but in my notebook case I'm too lazy to upgrade all needed applications from backports) for work (I use it for my desktops). Point 2 is excellent so called production or factory system (I do not want to bother with software classification and McFarlan matrix and so on). however it's not the newest it's rock stable with great functionality for home and professional usage. for me it's number one. I keep trying to test different distros but always go back to point
cheers,