Two ways I guess.
1) The holder doesn't have to be perfect, the magnets will draw the batteries into the holder so as long as you don't have the cradle cutouts too small, they will all touch eachother.
2) If you are using larger batteries than what this cradle holds perfectly, just scale it up .5% and you will have the same scenario I described above.
I guess I didn't do the trigonometry to make sure this would work for every size / type of 18650. I just designed it in 20 minutes and printed it in 30 minutes and moved on to my next project.
I've already made a replacement for my Dyson hand vac battery with it and all cells are touching eachother. I put a line of hot glue between them all just to be safe (Dyson did this on their stock battery packs as well).