to prevent the user doing something silly like trying to install GNOME but forgetting the X server and fonts.
I think the Package Manager copes with this very well, especially when the installation source is a release DVD. Unlike the network repositories, which can become inconsistant as individual packages are updated, the DVD presumably has gone through freeze and test cycles that greatly reduce, and hopefully eliminate, cases where some sets of packages cannot be installed because of unsatisfied or antagonistic depencencies.
If a user makes silly choices about what to include during initial Fedora installation, the result should be no worse than some missing applications, or extra files on disk and possibly additional choices that have to be made during use because multiple environments have been installed.
Perhaps it is the GNOME/X-server example, which seems to be precisely what package dependencies handle, that obscures the point you want to make.