Firstly you do realise that not all number '0' bolt heads are the same 'size', '0' is not a size it is just a number. I have seen a number zero bolt head of 0.616" and as big as 0.636" so 20 thou difference between them, the nominal 'cluster' of size zero (it is a bell-curve) is between 0.626 and 0.631, still 5 thou, which could make a big difference if your headspace is towards the top end of the spec.
How did you determine that you wantd a number 0 bolt head ?
Regarding getting it to 'clock' correctly the tool was used if it was just a few thou off being correct, some bolts / bolt heads would just not align as the start point of the threads can be 'anywhere'.
If you read Peter Laidlers notes on bolt head selection you will see that the Armourers would have trays with dozens of bolt heads and they would have to go thru them to find one that gave the correct headspace, and, the correct clocking. The chance of you buying one bolt head and it meeting all the criteria is fairly remote.