80s/90s story alien orphan that has itchy back and grows wings

It's ringing a bell for me, but I've not read Star Beast, so it may be there's more than one like it around.

Is there anything else about the story you remember, confusedcat? eg other characters, anything about the plot. Even a little detail might be the clue that helps us work it out.
Another possibility is Wings by Jason Lethcoe

When Edward’s mother dies, his aunt sends him to a school for troubled youths. There, Edward develops an itch in his back that he can’t scratch, and when he gets angry it seems like he can move things with his mind. When the itch erupts into a set of wings, an evil teacher tries to cut them off. Edward is rescued by Mr. Spines, who reveals that Edward is a Guardian, a magical being who guards and guides souls in the Woodbine, a stopover between life and death. Edward will now have to battle the most evil force in the Woodbine, the Jackal, and his army of fallen Guardians. They have destroyed the bridges that lead to the afterlife, trapping countless souls. Edward is unprepared for so much responsibility and he runs away and becomes lost in the Woodbine. There he must find his own voice and learn to master his powers as he is pulled from side to side by magical forces he is only beginning to understand
It makes me think of Star Beast by Heinlein
Me too. Even from decades-old memory, I can tell you that the large, perhaps apatosaurus-shaped, Hroshiia princess who collects John Thomases starts scratching at a bump on her side.

When John Thomas the maybe-Tenth tells her to stop, she says, "But it itches."

I think that line that she says in her high, squeaky voice (sounding like she had swallowed a very young girl, the story says), is verbatim.

With more scratching an at first scary-looking nascent arm or wing pops out, like a butterfly still wet from its cocoon.

Of course that happens symmetrically.
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Not sayin' it's the answer to the original question, but if Heinlein's The Star Beast is a possibility, here is the exact cover of the book I read and remember.

It's not an 80s/90s story. I mean, you can read it in the 80s or 90s; this version was published in 1975. ISFDB shows the first book going back to the 60s, and what looks like a short story before that.

She definitely itches, but grows new arms, not wings.

John Thomas calls her "he/him" because he does not yet know that she is a Hroshiia princess who apparently ran away from home -- until a delegation comes to bring her back to her people.
Flight in Yiktor also has a spiney "pet" and some sort of mental communication between some of the characters... if that helps the OP remember the story?