I've only visited the ANN site once, (prompted by this thread) but I gather that what it amounts to is that the legality of MorphOS is in dispute.  Whether it was created with reverse engineering, stolen source code, or a mixture of both seems to be the subject of contention.
Since very few people have any first-hand knowlege of the matter, it looks as if this will be a matter for the courts to settle, if the dispute gets that far.
As for the Pegasos boards running AmigaOS4, I understand that OS4 would require proprietary silicon, and that the proprietary silicon would require a license from Amiga, which license Amiga would issue if bPlan agreed to Amiga's terms.  I suspect Amiga's terms involve money, and a degree of control regarding quality standards and such.  Possibly more money, control, or both than bPlan likes.
Beyond that, I don't know.  (And from the tone at ANN, I am one of the few who admits it.)
;-) That's my take.  Your mileage may vary...