Of course they can track you to some degree either way, however the official app is using an IDFA (advertising identifier) [1] whereas Apollo is not, which makes tracking in the official app significantly easier.

The official app is also hoovering up other deanonymizing data like user location, which helps narrow down ad targeting even further. It's obvious why Reddit prefers you use their official app instead of a third-party alternative.

[1] https://en.wikipedia.org/wiki/Identifier_for_Advertisers