You can see the actual official requirements at the official Taiwan web site where you would apply for the certificate:
Online application for ROC Travel Authorization Certificate for nationals of Cambodia, India, Indonesia, Laos, Myanmar, and Vietnam
Nationals of Cambodia, India, Indonesia, Laos, Myanmar, and Vietnam
can apply online for an ROC ...
The American Institute in Taiwan confirmed by email that there is no Global Entry Enrollment Center in Taipei currently.
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From: AIT Non-Immigrant Visa Unit <VISANIV-AIT@state.gov> Date: Mon, 9 Sep 2019 at 01:30 Subject:
FW: Is it possible to have a same-day walk-in appointment at the
Global Entry ...
Summary: Not from a legal/policy perspective, as the restriction only applies to Mainland Chinese residents. It is difficult to gauge how that affects the ferry you are planning to take though (given there will be less tourist traffic).
The BBC article the OP linked contains a link to a notice by the Ministry of Culture and Tourism of the PRC. It reads:
For visits of under 30 days, you can now apply online.
Vietnam provides e-visas to citizens of 80 countries, Australia being one of them, if you travel by air. You simply apply online and pay a fee of 25 USD. It takes around 3 working days to be processed, and you can then download and print it to enter/exit the country.