Good to know, thanks @franksmcb. I tried @pallebone suggested work around using the Plank Dock, but that caused me to discover a new bug connected to Plank Dock, that I will need to report.
Plank Dock solves one issue. When you turn off "hide" function in Plank Dock the windows maximize correctly, never dipping behind the Plank Dock so that the bottoms of maximized windows are hidden. However, when you turn off Plank Dock "hiding" it doesn't allow you to drag a window to the lower screen vertically beneath it.
Keeping the "hide" function on allows you to drag windows to the secondary screen which in my case is vertically below my primary external screen. But this creates the same issue that I have with "hiding" the bottom Mate panel. It becomes very difficult to hit the right spot between the dual screens that will make the panel or Plank Dock reappear so you can use its functionality.
In going to report a bug for Plank Dock I found this one which is a different effect, but still a problem. There seems to be an issue with putting a panel on a shared screen boarder, which may be similar to the issue Mate bottom panel is having.
https://bugs.launchpad.net/plank/+bug/1539022
Here is the bug report I made for Plank Dock and linked to the Ubuntu Mate project too: