Yes every machine is just a bit different and depending on the stone being used that too can affect the hole size required..
On one cutter I cut my holes 3mm... On the other cutter I use 3.3mm.... So the thing to do is create a grid of circles... If using 4mm... I would start at 4mm, 4.1mm, 4.2mm, 4.3mm, 4.4mm and 4.5mm... My guess is one of those sizes is going to be the sweet spot for your cutter and your stones.
I like my holes just a whisker big... Making them too small and you'll have trouble... Making them too big though... And it doesn't look so good either... It's just like Goldilocks... You have to get it just right... But when you do... PRESTO... It works!
Kevin