There are many things that could go wrong, for example the package manager overriding those files if another package installs its stuff there (even if, in the particular case of entropy and portage, they should check for file conflicts), or the package manager leaving those files behind if one day you are going to remove GNOME shell, or you needing to manually update those files if needed in the future, and so on....
It is a package, since those files could be provided by a package already in the repository, thus it makes this practice dangerous and it must be pointed out.
That being said, if you know what you are doing and want to take the risk, since you think it is negligible, you can do it, it is your computer
