grammar - Usage of "of" in the following sentence

Gender inequality refers to unequal treatment or perceptions of individuals based on their gender.

This sentence structure, unequal treatment or perceptions, should be treated as if it is saying unequal treatment or unequal perceptions.

of individuals based on their gender is the prepositional phrase, and it modifies both unequal treatment and unequal perceptions.

Written in its expanded form, this sentence states, therefore,

Gender inequality refers to unequal treatment of individuals based on their gender or unequal perceptions of individuals based on their gender.

Obviously, this does not happen spontaneously; someone is doing it. In this case, someone is doing this to other individuals, but this is implied or taken for granted. If you want to incorporate who is doing what to whom, you can include the implied doer of the action by expanding it further. The doer can be someone, anyone, people, any 'other'.

Gender inequality refers to anyone's unequal treatment of individuals based on their gender, or anyone's unequal perceptions of individuals based on their gender.

If this does not clear up the confusion please feel free to ask me further questions in the comment section.