I noticed the ATO thing too. Spent a bit of time earlier in the week trying to work out what legislation (if any) has changed to prompt this update.
In addition to the Customs Act, you also have to read the relevant by-laws, which is where things like the $900 allowance (and pooling of family allowances etc) are specified. There is a copy on the ABF website (the relevant one is Customs By-law No. 1700571, about 1/3 of the way down the page):
Schedule 4 by-law
This came into effect in 2018 and does not appear to have changed. There is a table that lists various things that are considered "personal effects" (and therefore don't attract duty when entering the country). There's a few relevant items in the table:
Item 2 talks about personal effects that you took out of the country and are bringing back -- Exclusion 2.2 relates to things you claimed TRS on ("item 7 in the table in subsection 38-185(1) of the GST Act" referenced here is where you find the legal basis for TRS). This just means that you don't have complete freedom to bring a TRS-claimed item of any value back without paying any duty.
Items 8 (families), 9 (single adults) and 10 (single children) basically say that personal effects are anything else not fitting into one of the previous categories in the table that you bring in where the total value is under your allowance. There is no exclusion here to take TRS items out of the category.
My legal opinion is worth even less than yours,
@OZDUCK, but I can't see how anything has changed recently from how this has worked for years.
Besides, if they haven't changed the wording on the incoming passenger card (I think they are still using the yellow cards even with the new digital system?) then it specifically asks whether you are bringing in "Goods obtained overseas or purchased duty and/or tax free in Australia with a combined total price of more than AUD$900, including gifts?"
https://www.abf.gov.au/entering-leaving-australia/files/ipc-sample-english.pdf
Surely someone with TRS-claimed items under their allowance should still answer "No" to that question, regardless of what it says elsewhere on the ABF website.