This is incorrect. We are talking about government services. Language needs to be precise. There are cases where there is a difference between an individual, a couple, and a group of 3 or more. There is also a very tricky case for non-native speakers and those that are not aware of the culture from which these nuances arise.
The guidance must direct the implementors to use specific language. If confronting a situation in which a pronoun gives rise to ambiguity, do not use a pronoun. So, "if your service allows people to jointly apply for something," define it. Is it "your service allows two people to jointly apply," or "your service allows a group of people to apply," or something else? Using "they" is inappropriate. Something like "you and the other individual" is appropriate.