You're confusing two different types of installs, upgrades and clean installs.
- Upgrades upgrade the OS, copying a substantial amount of data from the previous OS's Windows directory to the Windows directory of the new OS. This in and of itself is the cause of majority of users' issues since Windows 7/8 drivers are copied over to the new install's Windows directory and system critical drivers (anything attached to, or integrated into, the motherboard) for Windows 7/8 are not compatible with Windows 10.
- Clean installs should be performed on a formatted partition, to prevent and rule out potential issues, at which point the user must perform all the steps previously spoken about (which the OEM did for the end user prior to them receiving their PC)
Windows 10, like any OS version before it, will run when an upgrade is performed, however you are guaranteed to have issues if you stick with the upgrade and do not clean install. Normally, you'd buy the new Windows OS and clean install, never bothering to upgrade; however, because Microsoft is offering Windows 10 free for the first year to valid license holders of previous OS versions, the device must be upgraded first to register the hardware ID of their device (pulled from the motherboard) within Microsoft's activation servers (this keeps you activated without ever having to enter a product key if you ever have to reinstall windows). Once an end user sees the "Windows is activated" under Settings, they should then perform a clean install.
With this being said, it is not Microsoft's responsibility to ensure users know this, however Microsoft has told users what must be done in order to clean install (mentioned above). It is also not Microsoft's job to ensure an end user is not running incompatible drivers or software. It is not their job to ensure or remind end users system critical drivers for a previous OS will not work on Windows 10, or to uninstall internet security software prior to upgrading, or to verify internet security software being installed is compatible with Windows 10. All of these things are the responsibility of the end user.
In reference to your question I quoted, Windows Update runs during the install for a number of reasons, but not necessarily to install updates. You generally only see this if you choose the upgrade option. I can't remember if it shows while within WinPE during a clean install, however if it does, it's likely it's verifying hashes or sending anonymous data about the install (i.e. errors, hash mismatches, etc.). If you used the media creation tool to download an ISO, it already has all current updates incorporated into it from the previous week's update release. These updates have been injected into the install.wim/install.esd and the process by which they're applied is entirely different than updates run from an installer from within Windows Updates.
- The one exception being the current ISO from Media Creation Tools may not be build 1511. 1511 was pulled almost immediately after being released to the public because certain code allowed for third party app developers to garnish far more personal information than they should have had access to. 1511, if not already pushed out again, should be pushed back out shortly in the coming days (this only affects ISOs from the Media Creation Tool, as you can download 1511 via Windows Update).