I have a cynical view, that no-one will ever be able to disprove, that there never was a geological barrier to constructing a second bridge and duplicating this section with the rest of the duplication/electrification project back in the 1950's.
My view is that the project ran out of money, and the excuse that "No suitble foundations could be found for the river crossing" is a crock. The replacement bridge over the Morwell River includes piles 36 metres deep(!) and even in the 1950's such an impediment would have been easy enough to deal with if a similar level of 'swampiness' was found there.
Perusal of VR records would indicate the duplication was terminated due to a lack of engineering capacity during the time of the construction of the north east standard gauge. There may also have been some redirection of already ordered materials. This was also the time it became obvious that the freight traffic foreseen, which was the driver for the duplication and electrification project, wasn't going to appear in the short term, and the necessity of duplication for capacity reasons was very low. That's not to say that the job was necessarily easy, just that it wasn't beyond the capabilities of the time.
Would DirtyBallast be able to quote some official government documentation, or a newspaper article, where they clearly claimed the duplication was cancelled due to "no suitable foundations could be found for the river crossing"??
Maybe DirtyBallast is simply repeating an old wives' tale that has no basis in reality.