They fit in smaller spaces, they weigh less, they are easily machine fed and tightened, use less material - and when you buy millions of them, all those small bits add up to a lot of money - so it makes sense from the manufacturers point of view, but not many others.There's no reason for these odd sized bolts from an engineering perspective, they only make sense from a dealers profits perspective.
Japanese cars, or the few I've had contact with, simply use Japanese metric standard which are different to European.
I did once get asked by a very senior VP of something important on the third floor of corporate headquarters in Philadelphia why I didn't design stuff to use all the same size screw so only one tool was needed . . . because the M6 screw won't hold quite the same as the M30 needed here, and the M30 won't fit in the space where the M6 is used . . .
But I too have two multi-splined keys for removing a Polo cylinder head . . used four times - once to get the head off, once to put it back, once again quite soon to get it off again, and one more time to put it back after having it skimmed this time . . .