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Edit /etc/dnf/dnf.conf and add an an entry for excludepkgs:

From man dnf.conf

   excludepkgs
          list

          Exclude packages of this repository, specified by a name or a glob and separated by a comma, from all opera‐
          tions.  Can be disabled using --disableexcludes command line switch.

installonly_limit= also works.

If this works for PackageKit or Gnome Software I can't tell. Lately PackageKit and dnf is now sharing a lot of code since Fedora 29.