Of course, their maiden titles were different, in that one was born a duchess of Oldenburg, the other an infanta of Spain. They also were obviously styled with different married titles, in that one became the queen of Greece, the other a princess of Bavaria. Evidently the "Mrs. Royals" tradition of names and titles is strong in Germany, insofar as women who married into the house of Wittelsbach were generally styled by their husbands' names (e.g. "Princess Adalbert of Bavaria").
So perhaps the fine point of the specific spelling of the birth name was irrelevant ... BTW: was the consort of King Otto of the Hellenes also a princess of Bavaria? I would assume so, but also that she was never thus styled -- much less with her own first name ("Princess Amelia/Amalia of Bavaria"). That would really have created a lot of confusion. Besides, I believe it customary to style oneself with the highest possible title.
So although her husband, born a prince of Bavaria, was eventually deposed and exiled from the Greek kingdom, he continued styling himself as "His Majesty King Otto of Greece" to his dying day. The latter designation was of especial importance, since he returned to the royal court of Munich in 1862, and had to distinguish himself from his older brother, King Maximilian II of Bavaria (who would have been styled until his own dying day as "HM The King of Bavaria").
By that logic, one presumes that his wife would have been "Her Majesty Queen Amelia/Amalia of Greece" until her death in 1875 ...