Hello Shannon,
I got really very excited when Mike mentioned the RFC!

I love Great War flying, but never get to talk about it on here as this is a Boer War site!
Anyway, I agree with Mike and I say that the uniform in the first photo can only be that of the Royal Flying Corps and nothing else.
There is a 679 Regimental Sergeant Major Frederick Milner Smithyman South African Service Corps listed in WO372/24 at the TNA Kew and he served in the Motor Transport section too!
I don't think this man and your great grandfather could possibly be two differant people, it is far too much of a coincidence and the MT section too! a perfect candidate for service with the Royal Flying Corps I would say, but this was in WW1 and not the Boer War.
If I were you I would have a chat with Audrey Portman
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you need to see his South African medal cards and check for any papers/medical file etc, this may well show any prior service, worth following up I think, he might have actually served in 26 Squadron RFC too!

Regards Frank