Am I correct to assume that the BMW sourced components are ISO whilst the Mazda gearboxes / engines are JIS.
I don't believe it makes any difference for spanners, the standards mentioned appear to apply only to max/minimum of hole sizes, the thread forms (metric 60 degrees), sizes, and pitches are the same across the standards and in nearly all cases (especially in the common sizes) the ISO and JIS dimensional limits are the same as well.
So in terms of spanner sizes, they will always be the same, and although it's theoretically possible that you could find that an ISO bolt wouldn't fit a JIS nut of the same size, the chances are so remote they aren't worth worrying about.
I'm afraid you are wrong about Mazda. They in a lot of cases use a different metric AF size for the nut or bolt head than that recommended either by ISO or JIS. I do not believe the AF dimension is more than recommended in the specifications. They also misbehave by not marking the steel specification on their nuts and bolts, all car manufacturers are guilty of that.
Mazda also has a habit of using both the "normal" coarse metric thread and the fine metric thread, therefore there are a number of nuts that will not fit on bolts.
I have a number of fine and superfine nuts and bolts in a special nut and bolt drawer unit in the garage with about 20 different fine and superfine fasteners in some cases different material specs for brakes and suspension.
Yes even Mazda, Subaru and Suzuki have their non standard moments usually about 10 minutes before you need to use the car when you have mislaid a nut.
