The App Store is but one cog in a large machine. Apple isn't 'losing' money because they definitely sold that developer a Mac and an iPhone.
If it were true that Apple is selling more hardware from developers and that brings in a ton of money to Apple, why would Apple have a $99/year requirement? That simply adds a barrier for a developer to submit apps to the app store.
No. There's no need to backup history of binaries. Majority of developers keep their repo on github (free plan). If they need to go back, they'll just checkout their git history.They probably need hefty cloud storage to back up all those binaries