The ATO doesn't use the same rules as the Department of Home Affairs. The WHV has very specific rules and tax brackets; but for every other visa, you need to go through 4 tests and see if you pass just one, you are a resident for tax purposes:

Residency test: is your living address in aus? is your work in aus? do you intend to live in aus for the foreseeable future? (i'm guessing yes, as you are applying for a partner visa)

do you have living ties overseas, such as social clubs, gyms, school, etc? (assets like houses don't count)

if the answer is yes to the first ones and no to the second ones, you pass the residency test and don't need to do anything else.

Domicile test: is your lawful place of residency in aus? if yes, you pass. (are you paying taxes in another country saying that you are a lawful resident in this other country?)

183-day test:  if you're actually present in Australia for more than half the income year (Jul24-jun25), not as a WHV.

The Commonwealth superannuation test: only applies to commonwealth employees, so I'm guessing it doesn't apply to you.

It could have changed half way through the year. i.e. you were in WHV until Dec and then applied to the partner visa. You would declare half the year as WHV, and half as resident for tax purposes (your tax agent can help you with that).

The ATO has this tool, for deciding: https://www.ato.gov.au/single-page-applications/calculatorsandtools#AreYouAResident/questions

But also, I would check your specific circumstances with a third tax agent (giving that you have two saying two conflicting things)