Hi there,
NSW BDM online index has a death registration for a Charles Robert FRASER but it seems that he died 28th January 1949 ( on the website there is an option to drill down to the exact date) and the death was registered in the Auburn district (a suburb of Sydney).
Ryerson Index also has the death as 28 January and in the Sydney Morning Herald of 29th
http://ryersonindex.org/index.htm Here is the SMH notice
https://trove.nla.gov.au/newspaper/article/18088347 SMH 29 January 1949 page 38.
You mention that the d.c. has been altered to show he had been in Australia for 47 years... Is that alteration formally initialled and acknowledged by NSW BDM or has it been altered by a family member during the course of their own earlier family history searches... If you are looking at an official transcription, has the transcribing service noted the alteration...
Not all ships came via Fremantle for their first port of call in Australia. Thursday Island was also a first port of call for ships coming via Torres Strait. And shipping from West Coast of USA was popular even before Federation (1901) and grew also after Panama Canel opened... 1913 ...
Not all passenger lists into Australia are extant.
Most did not need a UK passport to leave the UK until 1914
JM