While the new/edit @ProjectQuery@ form supports setting a secondary and tertiary sort clause, these project custom query settings are not obeyed when rendering the projects index view as a list.
The above is equally true for non-persistent @ProjectQuery@ sorting. In contrast to @IssueQuery@, when sorting by a column is requested (by clicking the column header), the previous sort clause isn't preserved and re-used.

Behavior is observed on Redmine trunk at r21194.

I haven't looked into this and I'm not certain if it's a defect or a not-yet implemented feature.