Frankly, the commander bit is really an anachronism they honour for old-times’ and Fleming’s sake. Today, a commander/colonel in any given branch of military is a senior-grade administrative post and/or a highly specialised weapons systems officer like a fighter pilot or submarine captain.
The kind of work Bond is supposed to have done - during whatever military service he arguably saw or not - today is done by NCOs, at the most lieutenants. A commander in a modern defence body is a character usually between 45 and 55 and chances are he spent on average already five to ten years behind a desk.
In Fleming’s day and age things were somewhat different - but then again not that different. Fleming gave Bond that rank because he had been given it himself. But Fleming was personal assistant to Admiral Godfrey and as such far higher in Admiralty nomenclature than any ordinary commando type in the field. And if Bond had been given the rank because of the nature of his business in his wartime service, as Fleming alluded in YOLT, it begs the question over whom to command with this nifty rank. When all we are given by Fleming are quick glimpses of fairly ordinary and highly dangerous assassination missions which no doubt Bond could and would have accomplished even with the rank of ‘dogsbody, junior grade’.
But really, who cares? Fleming’s main reason to make Bond a Commander Bond was that he liked to imagine things not as they had been but as they ought to have been. Bond is Commander Bond and relaxes not in front of the telly but at the casino. And when he bets on rouge the ivory ball ends up on red.