Mark You'll be able to add a blank website using the 'Start from scratch' flow.
You're not wrong, at the moment 'Install an app' and 'Add a WordPress site' do the same thing. In time additional applications will be added to the 'Install an app' flow.
'Add a wordPress site' exists to allow customers to sell packages that have WordPress preinstalled and for it to be clear to user that this will be done. You can prevent 'Add a wordPress site' on a package level by setting 'Pre-install application' to 'None'.
Hope this helps