Did the Wright brothers discover the three-axis control system for airplanes/gliders and the adverse yaw?
The patent lawyer is explaining things quite correctly and this applies to modern aircraft.  The rudder does in fact have nothing to do with steering the airplane.  Its job is to keep the tail lined up behind the nose (or to move the tail out of alignment with the nose if you wish) mainly overcoming adverse yaw caused by warping (or later, ailerons).

The bolded text in the paragraph you quoted describes the wing warping being for roll control, and the rudder for controlling for the adverse yaw that results from the wing warping (same as aileron displacement in modern aircraft), just like any modern aircraft.  He is describing how a modern airplane flies in other words, and this was a pretty radical idea at the time so it didn't make sense to a lot of people.

The Wrights discovered adverse yaw as they were developing their totally new wing warping system concept, as it was abundantly obvious from the way the nose would slew the opposite direction to the wing warp input and a rudder control was the obvious solution.  They didn't get it from anybody else because nobody else had thought of the concept of differential lift to control bank in order to turn.   Lillienthal, from whom the Wrights based a lot of their work in the beginning, used weight shift to control his gliders. 

I recall from books I read on the Wrights years ago that they proceeded originally from from Otto Lillienthal's aerodynamic theories, and as they tested their glider machines, they started to discover that Otto had a lot of things wrong, prompting them to build their home made wind tunnel and start development from scratch.

So I would say for (1) yes, they invented the 3 axis control system, that is, all 3 being used together to make coordinated banked turns, because they developed and patented wing warping (ailerons coming later and leading to a long patent legal battle with Glenn Curtiss).  Up until then, and for some time after, developers were controlling turns by skidding using rudders (helped by dihedral effect to achieve banking in some cases) or by weight shift, or in Bleriot's case trying to achive roll control with differential elevator movement like an F-15 to get around the Wrights' wing warp patent (which they defended furiously, leading to the long patent battle with Curtiss, who ironically ended up taking them over in later years and becoming Curtiss-Wright, a running concern to this day).

The proof of this is obvious if you read of the various accounts describing the Flyer's demonstrations through the mid 00s.  The Flyer's contemporaries, such as they were, would slither about the sky, whereas the Flyer flew around making coordinated banked turns like a modern aircraft.  This astounded observers, especially the French when the Wrights demonstrated the Flyer in France.  The French reaction to the Flyer was really something else, one of awe, admiration, and a bit of jealousy, that those two American yahoos brought a flying machine that could literally fly circles around machines like 14-bis.

So for (2) I would say the answer is also yes because they invented differential lift for roll control in order to turn, which quickly indicated the need for a rudder to counteract adverse yaw and which followed on naturally.