To my knowledge, the English manga releases are pretty much straight-up translations of the Shougakukan volumes. The "Three Wishes" sidestory you mentioned is in volume 3, the Black Rose and Ruka sidestories are in vol 5, and Adolescence is its own self-contained volume.

The three-volume bunko release seen a little further down on both sites you linked are a condensed rerelease of the original manga volumes, with a smaller trim size and higher pagecount per book, and all the sidestories and Adolescence are crammed into the third volume (which is over 400 pages!) along with the last bit of the main manga storyline. Bunkos usually don't have the author's sidenotes that regular manga volumes have, but these ones do have little essays in the back, which I'm actually a little curious about myself.

I hope that helps!

Oh, okay! Thanks!

I too am now interested in those essays... I wonder what they could be about? If someone hasn't already translated them, perhaps I could buy those volumes myself... And I didn't know that Adolescence was the movie manga... That's kind of stupid of me.

So, I have another question: do any of the Utena plays differ from the source material? I know the second one has the zombies... but are they all just essentially condensed versions of the anime/manga?