The magnets getting embeded on layer height 0.4mm to 3.8 mm so there is some play that they have enough room. When Slicing with prusa slicer on 0.2 layer height settings you can at 4.00mm put a break.

The holes are 5.5mm in diameter so it's easier to get them in. there are 6 places in total 

If you need any custom sizes, i can try make them if they are not to crazy it should be relativ easy to change.

I added them as material, i did use some random from amazon.