Well, in all honesty Fleming never really indicated Bond would be anything other than an Englishman pre-OHMSS. The entire canon up to that lacks any personal references to Scotland (or Switzerland for that matter). One might chalk that up to Bond not having lived with his parents long enough to assimilate any 'Scottishness', but his aunt Charmian would have been probably as Scottish as his father had been, wouldn't she?
No, the fact remains that Fleming just made the background up as EON and Connery came along and he, in spite of his initial doubts, was impressed by Connery's depiction.
Actually, doublenoughtspy debunks this this long held belief in his book The Making of On Her Majesty's Secret Service. He discovered correspondence that shows Fleming planned to give Bond a Scottish background (like his own) in 1960, two years before Dr. No. This was in correspondence between Fleming and the researcher who helped him create Bond's background for OHMSS (and who came up with "the world is not enough" motto).
As you might know, Zen, I am a huge fan of Charles book, but even Charles does not make it the factual statement you make here. Charles uses the word "considered".
Doublesnoughspy gives evidence of 1960 correspondence in which Fleming asked an historian to look into a Scottish Bond family line which he cannot find, though he conceeds that does not preclude there being one.
Charles further provides evidence of a quote from Fleming on Connery's casting in which he approves of everything about Connery EXCEPT his strong Scottish accent.
However, neither of these insights change the facts: in the novel he wrote imediately after the Scottish-heritage research - The Spy Who Loved Me - Fleming makes no reference to any Scots background, and that James Bond only came to enjoy a Scottish heritage AFTER he had see Sean Connery in Dr No, during which it is perfectly possible Fleming overcame his reservations about Sean's accent (which was toned down from his then-brogue anyway).
It is all speculation, one way or the other. However, I think there still isn't enough evidence to suggest that the Scottish-driver was anything other than Sean Connery...