I believed to have found a bug in the MATE panel just to file it on their github issues list and to then find out that it is actually the expected behaviour. Let me explain: I have the MATE desktop installed and made a new panel that autohides. Also, I set transparency to 100% (fully transparent) via the settings window on right click. Now, when hovering (and it popping up) the background is taken from the desktop's background, not the highest window on screen covering the location. I was told (as you may find if you read the linked issue), that I should set the window manager to compositing. Actually I tried both but none of them is working so I ask you, how can I set the pseudo-transparency to real transparency?
EDIT, Aug 14: I found this quite similar question. As far as I understood correctly only some (non-nvidia) graphics cards are supported. FYI: I have an ATI Radeon HD 5470, 512 MB. Still, if you can provide me with a solution I'd be very happy.