Just to add my six penn'orth.
There is still a requirement to fix your position using radio aids while IMC - it's just been moved from the nav phase into the IF airwork phase for the reasons already stated - the JAA CPL gives no IF privileges. However, the IFR fix is still part of Section 3 (En-route) so if it goes wrong it's the nav that you'll be repeating plus a bit of IMC at the end to re-do the fix.
The second leg of the navex IS worth doing - it tests the ability to plan in the air rather than just follow a preplanned, pre-studied route.
Whatever Oxford choose to teach in their syllabus, the test is done by an examiner who, for integrated courses can be an OAT instructor, but who is working on behalf of the CAA and so should be following the same guidelines as any other FE CPL - OATS can't lay down what happens on a CPL Skills Test!
The reason the IF work is still in the test is primarily because ICAO requires it for any ICAO compliant CPL.