No country is going to deny your valid citizenship application simply because you haven't chosen to retain your South African citizenship. It makes no difference to them whether or not you choose to retain your SA citizenship. Unless they have laws which prohibit dual citizenship, in which case they will want evidence that you have in fact given up your SA citizenship, otherwise it makes no difference. Please show me on the Australian government website where it says you have to supply information regarding your SA citizenship status? This idea that foreign governments report it to the South African government is simply not true.
Even if you don't want to tell us which country you got your citizenship from, just a link to one form or government website which makes this 'letter' from home affairs a requirement would convince me I'm wrong.
No one has said they will deny your citizenship application. Not sure where you are getting that?
What is being said is that unless you first apply to retain your SA citizenship and include the letter in your application, they inform the SA government and you lose your SA citizenship.
As for online forms, I have no idea. I applied manually at the embassy.
For applying for Australian citizenship, this has already been posted in this forum
https://www.sahc.org.au/citizenship/Dual_Citizenship.htm
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