How would a student justify inferring that “indigenous” means “originating in a particular region”?

Traditionally, indigenous comes from the Latin word indigena (indu/endo: in/within + gignere: to beget (to procreate or generate). But here we are simply looking at roots. The root words here are -gen (something produced, and by extension, birth) and -ous (possessing/full of), and that combination is not an option, it seems. HOWEVER, it is not uncommon for suffixes to have more than one meaning, and this is no exception. -ous also means 'having, full of, or characterized by', meaning your answer is the second option, 'the word root “gen” means “birth,” and the suffix “-ous” means “having the quality of something.”'