Yes, prioritize flashcards is checked for "words containing" but not for "words beginning".
Now that I play with it a bit, I think what I am seeing that if I search for a specific character then on the "words" tab, it does seem to sort based on flashcard words, but if I search for a word containing a specific character, in the right tab where the word is displayed, if I click on one of the characters in that word, then use the "expand" arrow in the top left, I get a pop-up with just that character, and the "words" tab for that is not sorted according to flashcards.
In the legacy version, if I clicked on an individual character within the word, and used the arrow on the bottom left to take me to the definition page, that definition is overlayed in the same UI element which inherits the same behavior as the definition for the whole word. FWIW, I did like that better than having the smaller pop-up window, but I guess my main concern is that there isn't symmetry with respect to the sorting order.