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The virtual java package depends on at least one out of the java package.
Gentoo allows that different versions of the same packages can be installed at the same time. However saving 100MB less compared to the rest is not worth losing the documentation.
The reason why it is here at the beginning, is to prevent that you make a mess in your installation.
If you read this book the first time and you understand none of the commands, just skip it.
However some ebuilds install also binary packages and others even debian deb packages.
Once the https:// web site contained a lot to browse and search throughout portage, but it disappeared due to a security issue.
If you loose this file you can recover some of it, Usually emerge takes the newest stable package (e.g. Packages can be hard masked by the Gentoo developers.