I believe any clearly visible dirt will subject the bike to more extensive cleaning at shipper´s cost. The advice on AQIS website is ´clean as new´.
We washed our bike for several evenings in Indonesia before sending to Perth, taking off all fairings, fenders, fuel tank, etc., and I actually renewed the air filter at the same time, making sure it wont give us trouble.
Actually I think we got lucky, because the inspector at Perth airport seemed to be in a kind of hurry, and so checked the shipment, while it was still inside the crate, lifted up by a forklift... but we got a notice about the tyres, that had just a very very minimal amount of sawdust, which must´ve attached to them, as I pushed the bike about 5 meters from where we washed it for the final time, to where it was put in the crate! But he still let it go without more cleaning.
So yeah, it seems quite thorough, and I believe usually they are in no hurry. So I´d get rid of every trace of any visible dirt no matter what, and also clean everything from the inside, that you´re able to clean without major overhauls.