Sometimes due to availability and price you have to modify something .In this case i just couldn't get 10 potentiometers with the required length and flat side from the supplier, so i had to settle for round shafts that were too long.
It can be alot easier to sort of automate the process and worthwhile to make a jig.You can see the end profile here all i did was make a square block of wood then using a pillar drill bored a 6mm hole down the centre.
The block was then cut just over the halfway mark longways then you end up with a nice slot to hold the shaft in the correct position and height.
Adding a metal plate allowed me to adjust where i wanted to limit the flat on the shaft also holding the shaft in the correct orientation!
And what you end up with is 10 perfect flats with the same reference point when the knob is turned from one end to the other .