Why does Duolingo seem to prefer the तू pronoun?
I almost never hear this being used in India and have been told it is disrespectful outside of extremely close relationships.
Why not use आप or even तुम?
You are absolutely correct. Be it Hindi or Urdu, we don't prefer the use of 'tu'. It is completely disrespectful. You should better stick with 'aap' and 'tum'. As for your question why Team Duolingo chose to teach the informal and lesser used 'tu' is a mystery.
While beginning to learn, it is easier to start with तू because it conjugates similarly to the third person singular pronouns or nouns. But I agree that it should come with some kind of 'usage note' inside the main lesson because not many people read the 'tips and notes section' (not to mention that it isn't accessible from all platforms).
I thought this when i started to learn, I was lucky to have a native speaker who told me the difference between the different types of 'you'. I have no issue with Duo teaching it but there should be an asterisk or a little note somewhere to give a heads up about the differences. It would be a big insult to use it where you shouldn't.
When translating from English to Hindi, I got into the habit of always using आप or तुम. It is accepted as a correct answer almost everywhere. तू will only be shown as an alternate answer. If in the other direction translating to English, तू is regularly used especially in the first lessons, but it seemed to happen less in more advanced lessons.
The imperative tense, though, is built on the polite तुम, for example खाओ. I didn't see any informal imperative anywhere (खा), which would be even more problematic to use inappropriately than the indicative.