These settings are global in what used to be called Internet Config. The Internet panel in OS X is clearly incomplete compared to the MacOS one, however you can still edit these prefs using IE 5.1 which edits these global prefs.
(by global I obviously mean per user)
Whether OmniWeb uses these settings is another matter. Any mac app using url links will. For example if you make a link like:
carracho://server.com:6677
In IE 5.1's url bar and drag it into a Drop Drawers X drawer it becomes a link you can click. When you click it Carracho will launch.