At the top of the page describing git installation, it says "This would not be suitable for app development, but is suitable for contributing to the framework.". The git installation is intended for contributing to the framework, *not* for app development. With the git installation, you would normally "git pull upstream master" if you are updating to the latest release, and with "upstream" referencing the main repo ("origin" referencing your fork). If you are developing your app with this clone too, then yes you will have to deal with merge conflicts every time you update. It sounds like you didn't even fork it, but instead cloned the repo directly, so you wouldn't then have a github repository, and "origin" would reference the main repo.
The manual installation is pretty much the same, except that you download the latest version to a separate folder and then manually merge, without merge conflict warnings. This is the "old school" way, from CI3.
For app development, the composer installation is intended to be the easiest way to upgrade... "composer update" and then check anything mentioned in the release notes as applying to the "app" folder.
