Earlier quoted context omitted.
Nobody's permission is required to write apps for your own iOS device.
Maybe not to write them, but to run them you need Apple to sign them. A free developer account can be used to have Apple sign your app, but then Apple will only give you permission to run that app for 7 days, and only give you permission to install 3 apps signed that way at a given time. In any case, side loading iOS applications absolutely requires Apple's permission. Unless you were talking about jailbreaking.
Freedom to modify is not the same as zero cost. You paid for the iPhone hardware, after all. Just pretend it cost $99 more and came with the right to load your own apps.