While I cant speak of this incident as I dont know any more than the ATSB report - I have had several situation in GA where a clearance was required and ATC weren't keen... until i told them what was happening. A phrase as simple as "due weather, request clearance direct ..." was enough to get a clearance organised - not necissarilly immediately (due IFR traffic or similar) however actually talking to the controller and telling them what you need can make all the difference. Now that I work in an IFR RPT capacity, i do not know a single pilot that I work with that wouldn't mind burning an extra 5-10 minutes of fuel to allow a VFR aircraft through/infront in marginal weather if we're in the way. We can fly through it... they can't.
In some situations, even the old "we have this issue, we are doing this" was enough to make things happen, the paperwork can be dealt with later - and if you have a good enough reason to do your own thing to stay safe... then you're good.