Thank you for the added information about the use of rubble as ships' ballast.
Looking at the quote you have, I suspect that the journalist may be describing the shape rather than the material of the railway ballast, but I agree that it's a possibility worth investigating.
I've had a brief look into the flint mines of southern England, looking for likely sources of the exported Thames flint. My working theory was to find a source of flint worked (relatively)recently, and then look for small or industrial railways in the immediate vicinity. Unfortunately most of the information readily available online concentrates on the prehistoric mining of flint, not its use in the industrial era.
One likely candidate I found is the
Chislehurst Caves. These were apparently worked up until the 1830s. This would easily be late enough for flint rubble to be shipped out to the new(ish)colony of Australia, but predates the advent of the railways. There could have been tramroads used in Chislehurst before then, but I can't find any evidence of them. (Furthermore, I've no idea off-hand what sort of substrate early tramroads' tracks were laid upon.)
Without finding a source of British flint that was still being worked in the Victorian era, I doubt we could find an example of a British railway using flint as ballast. But given the desirability of ballast made of irregular, angular stones, and the fact that local stone would be used wherever possible*, I have no doubt that flint ballast
could have been used in Australia.
*A little closer to me, the use of waste slate chippings for ballast is common on (industrial) lines throughout the slate-quarrying areas of North Wales.