Mostly, because article is mashup of random data things about Facebook, and it's not clear what is being investigated. They started that phone makers data deals

Mostly, because article is mashup of random data things about Facebook, and it's not clear what is being investigated. They started that phone makers data deals are being investigated (which is basically alternative client), then goes into Cambridge Analytica, and mention Bing data access in the end (which could be about deep access you are talking about, but it does not looks like it's being investigated). And for phone deals, criticizing friends/deep data access... If you want to build alternative FB client, your phone have to have access not just to your data, but also to your fiends data (i.e. all data you have access), in order to provide any useful service. So yes, technically your friends didn't agree that your alternative FB app can access to their data, but you gave your access credentials (and permissions) to access that data to your phone.