Hi Elizabeth
I have found so many of my family myths - have in fact been myths - that I tend to ignore that side of the story & concentrate on what is known.
If he died at Fort Augustus while working there - was it an accident? Did he go to Hospital? Is it possible that a inquest/autopsy was required. This may have meant his birth was recorded perhaps somewhere else.
My mum lived in a country town but when she became ill was flown to a hospital 400 miles away - hence her death is recorded somewhere very different to where she lived.
When was he born? Can age at death help the search.
Are there any known problems with the death records of this time? Did the war impact record recording.
If you are checking from 1900 - Is he on the 1901 Census?
Then again, Annie's suggestion may resolve it very quickly

Trish