[Cottser]

The setting of the handles can actually be tweaked in the theme file. The easiest way I can think of to make sure your custom theme is not overriding the defaults is to open the ofocus-theme file in something like Apple's Property List Editor or Pref Setter.

Then look for this key in the left column:
item-handle-mode(com.omnigroup.OmniOutliner)

As far as I know, the possible values of the key are "always", "hover", and "never". So for example, if you want the handles to show up, change the value to "always".