It is still a yes/no question, however, it is stacked. It is asking "is it pink? (Yes or no?) or is it purple? (yes or no?) Just like in English, replying yes or no is confusing.
You are right, though, in that it has an altered meaning.
Ĉu is the yes or no question, is it true that...?
Ĉu (a) aŭ (b) is the comparison question is it (a) or is it (b)?
Still a form of question, but they require different forms of answers.
Just putting it out there.