Is there a reason for srcdir and repository to be put into the home dir by default? Especially the srcdir seems to be misplaced there because it looks, smells and usually has the same name as the clone you want to generate exactly there to edit the wiki on the command line. Both srcdir and repository should usually be left alone and that doesn't sound like the files you would want to place highly visible into $HOME
Sure, I have no problem relocating the dirs myself or editing/replacing /etc/ikiwiki/auto.setup whenever I reinstall a new PC, but a better default would spare me and others a bit of work.
To me it seems $HOME/.ikiwiki/ might be a good default for storing all this essentially-to-be-ignored dirs as it is created anyway.