How to setup module install (sub-folder) paths from the *very beginning* (contrib, custom, features etc) - i.e. not move them after the install
Actually it seems like all you need to do is just create a folder called contrib in /sites/all/modules

when I issued drush dl views (at the docroot/install top level root of my site), drush put the views module in the contrib folder

as for features - you specify where you want the module to go when you (re)create the Feature (in the Feature section of the Drupal config)

as for custom - I'm hoping that Drupal will discover custom modules here - but is discovering, rather than a setting determining the path, a good thing?

Thought I'd still ask the question even after I'd found an answer, didn't want to waste the effort in making the question - hope someone else finds it useful. 

Please provide your own answer or comment to enhance what I found.