Spotify Premium account price on App Store
It's a simple marketing ploy.

Apple Music is $9.99 a month

Spotify is $12.99 a month, through the Apple Store.

Spotify want to match Apple's price, but don't want to cut their revenue to 70% of $9.99, so they're offering you $9.99 direct, rather than $12.99 through Apple.

That means for every person who changes to the direct method, Spotify actually receive more than they used to through Apple.