Yes, Apple does have the power to change every bit on your hard disk if you let it. Things like EULAs are supposed to govern to what extent they can use that power.
Please help me understand this. Where in the EULA or elsewhere have users allowed Apple to remotely install a U2 album, or delete third-party software? What of the fact the EULA itself can change at any time without any posted notice? Or worse, what if Apple is forced or breached to deliver a "security update" which steals personal information or bricks your device? Why is this not a legitimate concern to technical professionals? Or, where is the documentation which at least explains this behavior to put curious minds at ease?