By that logic Apple does not prevent end users from rooting the phone and installing anything they like, it just makes it very inconvenient... and less shady than Microsoft's shell execute bug.

If we assume for the sake of argument that a particular customer would knowingly buy a computer from an OEM who pre-installed Netscape on it, then the OEM is the user of the computer before the end user buys it. Why should Microsoft be allowed to prohibit such a pre-installation? For security, maybe, but that probably wasn't Microsoft's motivation.