I had the same question, actually, but eventually realized that you can tell the difference without worrying about the il/ils pronunciation. The singular conjugation of the verb would be "fait", e.g. "que fait-il seul", if it were singular, so the use of "font" means it must be plural.
I wonder this as well. I answered "what do they do alone?" and it was accepted as correct but Duo gave "what are they doing alone" as an alternative answer. My answer is focused on what they are doing, whereas the alternative Duo gave could be interpreted as questioning why they are alone (e.g., why were those children left alone without adult supervision).
"font" = French verb "faire" = English verb "to do"
"what makes them lonely" is a different sentence construction that is covered in the next unit Pronouns 1. (see Duo Tips and Notes https://www.duolingo.com/skill/fr/Pronouns-1/tips-and-notes).
I think that you could translate your sentence as something like "Ce qui les fait se sentir solitaire ?" or "Ce qui les rend solitaires ?". In your sentence "them" is the object of the sentence and the subject is the thing that is making them lonely that the sentence asks about. In the Duo sentence "they" is still the subject of the sentence, and the question is about the activity they are undertaking, or the reason why they are alone.
If any native French speakers or English grammar experts can offer more help please chime in!
If you start a "what" question with "que", one way is to use inversion (que font-ils). Another issue is that "que" may mean "what" or "that"; it would be contracted when the following word begins with a vowel but I don't believe you can contract it when asking a "what" question, except when using "est-ce que", e.g., qu'est-ce qu'ils font seuls ? Here we see the contracted "que" in its two different meanings. For more on how to ask questions in French, open this link in a browser: https://www.thoughtco.com/questions-in-french-1368935
Que elides and becomes qu' when the following word starts with a vowel sound (see info under Elisions here: https://www.duolingo.com/skill/fr/Basics-2/tips-and-notes).
You could also say this question in French as "Qu'est-ce qu'ils font seuls ?", and in this case "que" is elided in front of "est" and "ils" because they both start with a vowel sound. In "Que font-ils seuls ?" "font" starts with a consonant so "que" doesn't need to change.
They and Alone, wouldn't they be together instead of alone, sort of an oxymoron in translation.