Hard to believe. Duo doesn't make us write "You all" whenever there's a plural "you", but will list "You (sing.)" or "You (plural)" on specified forms of You. It'd be no harder to list singular "They (sing.)" as a translation for yeye, it would make it so it doesn't arbitrarily discriminate against gender diverse people, and i think clarify understanding that it's not a gendered term.
that's because even in English, when you're referring to 'you' plural, you don't have to say 'you all', and the more common version of that is 'y'all', which is largely colloquial. In addition, 'they' as a singular gender neutral term is not universally used (especially in English speaking countries outside of the US and the UK), so yes, 'he' or 'she' is used to clarify singularity. This course is meant to provide you with a foundation for Swahili, and gender neutrality just doesn't translate the same, because unfortunately Swahili doesn't have established gender neutral terms; this case is pretty much happenstance. From the many notes we have provided for this course, it has been addressed that 'yeye' is singular in the 2nd person