That might be because since 1969 (from memory) it has been the RAN practice to drop the flag superior "A" and use part of the type designation "O" for "Oiler" or "OR" for "Replenishment" in small letters before the number on tankers. Choules, LHDs and the hydros OTH have the flag superior painted up (although it's a small "A" for the hydros), while of course the DDG/FFHs, Armidales and Huon (whose flag superiors are D, F, P and M respectively) have nothing.
Prior to about 1969 everybody had their flag superior in large letters, eg HMAS Vendetta had "D08" painted up (in the RN position and black paint before about 65, white paint and the USN position after that). It changed to plain "08" in '69 or so. So the painting of Supply (and, presumably, Stalwart) are departures from recent practices or a return to earlier practice, depending on you point of view. I wonder if the combatants will get theirs back at some point as the wheel turns further?
So we're not used to seeing the large "A" although there is a photo of the real battle tanker wearing an A in her Wikipedia entry, here:
File:HMAS Supply Brisbane 1967.JPG - Wikipedia. Interestingly, there are also photos is existence of her wearing "AO195" in dark colours and the RN pennant number location. Not sure when that would have been, although before 65 I imagine.
Who said we had to be consistent, anyway?