It's because Apple's actual costs are pretty much fixed (storage, bandwidth, ...) so clearly on a low price / many customer scenario it seems fairer.
That's why a per usage pricing would be fairer. And yes, the app having one thousand $10 purchases would pay way more than the app having a single $10000 purchase, but that's the point.
But for Spotify or other apps that sell content Apple is not providing storage, bandwidth, or anything else. They do provide payment processing, but it's common for that to be a small percentage of purchase price already (e.g. ~1-2% for credit cards).
That's why a per usage pricing would be fairer. And yes, the app having one thousand $10 purchases would pay way more than the app having a single $10000 purchase, but that's the point.