The highlighted checkboxes are so-called three-state-checkboxes. In the highlighted form those are in the indeterminated state, i.e., TortoiseGit does not explicitly activate or deactivate those options, but uses the default of Git.
TortoiseGit uses the three-state checkboxes here, so that you can override the default which is configured in vanilla git (there are several ways in git for configuring this, e.g. fetch.prune, remote.<name>.prune and maybe others).
In order to change the default you have to use git config.
For controlling the default value of prune see fetch.prune and remote.<name>.prune. For controlling the value of tags see remote.<name>.tagOpt.