How is it going and how are you doing are synonymous in English, but the latin quomodo tu te habes literally means how are you feeling/doing.
How is it going in English means more; how is your life progressing, and how are you doing means how are you feeling.
Hope this helps.
The point of a beta is to fix bugs and sort out translations, which they also count on learners (course takers, rather) with substantial Latin knowledge to submit alternative translations and point out mistakes committed in the course. If you're certain that they accidentally one of the translations, go ahead an submit a suggestion for them to use.
Maybe the course creators just want a few exercises where they use "tu" so people learn the word, and know that it's an option. It is rarely used, though, from I understand. (Please correct me if I'm wrong. I am new to Latin.)
Also, it's not that hard to remember for anyone that has studied French, Italian, Portuguese or Spanish which all use "tu" ("tú" gets an accent in Spanish) as a second person singular personal pronoun, albeit limited to a "familiar" sense.
English even has "thou," though it's archaic for most modern native speakers, I believe.