QueenAlice said: "Moving forward, will stock companies that want to explore non-binary casting receive any push back from rights holders?"
If the text isn't changing at all, it doesn't really matter how a community/school/stock theatre casts it. The casting descriptions are for the characters, not the actors who play them. Similar to casting a 50-year-old actress as the 18-year-old Anne Egarman, or a Black countess, or a soprano Desiree (with MTI's transpositions on demand).
If this were a major regional production, things might be different. And would certainly be different if this was a first-class production that went through the Sondheim & Wheeler estates.
Sondheim (and even more so Hugh Wheeler) must be rolling in his grave with them calling it "Stephen Sondheim's ALNM."