To answer your questions, starting with your last one:
Losing and retaining/reacquiring Philippine Citizenship
Per Philippine Commonwealth Act. no. 63 (section 1, paragraph 1), you automatically lost Philippine citizenship when you became Australian (the quote is from Lawphil.net):
Section 1. How citizenship may be lost. – A Filipino citizen may lose his citizenship in any of the following ways and/or events: 1) By naturalization in a foreign country;
The Philippine Dual Citizenship law (RA 9225) amended the Commonwealth Act 63. In effect, it created a "work-around" for this by creating a provision for natural born Philippine citizens to "retain or reacquire" Philippine citizenship:
Section 3. Retention of Philippine Citizenship - Any provision of law to the contrary notwithstanding, natural-born citizenship by reason of their naturalization as citizens of a foreign country are hereby deemed to have re-acquired Philippine citizenship upon taking the following oath of allegiance to the Republic: [took out the oath in the quote]. Natural born citizens of the Philippines who, after the effectivity of this Act, become citizens of a foreign country shall retain their Philippine citizenship upon taking the aforesaid oath.
If you haven't gone through this procedure, you are legally no longer considered a Philippine citizen. In order to be able to "keep" or retain Philippine citizenship, you have to go through the procedure of citizenship retention (which may seem like an administrative formality, but it is something you legally have to go through).
In addition, per the website of the Philippine Consulate General in Chicago, the moment you became Australian, your previous Philippine passport was considered invalid (even if it was still valid on the passport):
The moment you were naturalized as a US [in your case, Australian] citizen, you have relinquished all your rights and privileges as a Philippine citizen, which includes the possession of a Philippine passport. As such, your Philippine passport is no longer valid.
Only after going through the procedure will you get what's called an "identification certificate" which allows you to get a Philippine passport again.
Thus, in your situation, if you try to leave the Philippines with your Australian passport, you most likely will be subject to penalties (even if you are a Balikbayan, you are still technically considered a foreigner, and subject to the same penalties; per the link in this previous post here on Travel Stackexchange, these might go up to PHP 18 000).
In this case, I think you have two options:
- Go to the Bureau of Immigration office in Intramuros, Manila, and get the visa extended before flying out.
- Go to the airport on the day of your flight, and pay it there...with the possibility that they might tell you to go to the Immigration office anyway.
(Looking online, it seems that this is possible but I cannot find any official page that says you can do this. They also say that they might make you go to the Immigration office anyway).
Unfortunately (and this is my opinion), I think you have to be ready to pay the overstaying fees.
You could process your Philippine citizenship retainment/reacquisition (if you have all the paperwork ready) before you leave the Philippines, and maybe (this is a BIG maybe), they might consider reducing the penalties/waiving them. I am in no absolute terms saying that this is a certainty and have no official proof for this. But it seems that there are no official guidelines for this.
(In the in-Philippines page, from which I got the information on the fees, there are many comments made by dual citizens. For example, check the comment by and the response to "Vanjoe Colado", from 12 November 2018).
Hope this helps.