I don't personally think they're likely to be bad enough to warrant a change of itinerary.

You're right: they're not a problem in Sydney (they might be if you had a picnic in a big park somewhere, but for ordinary activities they're not), and I imagine the same goes for Melbourne, as you say.

Elsewhere, use some insect repellant (I like "Rid", which comes in a roll-on form, which is convenient), though go to a pharmacist when you get to Australia and ask advice there. As I say, avoid eating outside in bushland or parkland if you are worried about flies.

Although they can be irritating, flies in south-eastern Australia are nothing like as bothersome as, say, the midges in Scotland in summer, for example, and I've never avoided going to Scotland because of midges.