The solution is in fact very simple. All you need is some sort of a spacer of proper size and thickness (let's say 2 or 2.5 milimeters thick) to put it between a stone holder and a stone.
Where to put this spacer? Check the red arrow on the photo from the link.
How to fix the spacer? Double sided tape.
-Someone not so handy could use something already mad and don't need cutting to proper size and grinding to proper thickness - a screw washer, coin, piece of plastic or whatever
-Someone more handy could cut himself piece of proper size from brass or aluminium
Do I fix the spacer on the stone holder or on those stones with 3mm thick blanks?
I would say on stone holders. I suspect the holders will still hold the stones with 5mm thick blanks just fine.
https://drive.google.com/file/d/1It8S7JQO3YFrZja4BGemiqbXuGQ_5ktU/view?usp=drivesdk