I loved the magnetic Dice box from @VEECH [ https://www.thingiverse.com/thing:2974040/remixes ] but my d6 dices didn't fit (the almost sharp edges 16mm variant).
I used the original for a few weeks, pushed the d6 in by force and drilled bigger holes for the 5x3mm Magnets I still had.
Now that my cleric frequently needs d4 and d6, I thought it's time for a new case that fits better - but instead of adding a 16*16 square cut to all hexagons, I noticed I could fit 1 more d6 and also extend a few holes so the d4 lies flat. This also allowed to reduce the height of the assembly by 3mm (bottom 1mm, top 2mm).
I also extended the magnet holes to 5x3mm.

Note: some D20 dice have a height of ~19,7mm, others are ~18,8mm.
Keep in mind you may want to add some foam/fabrick sticker to reduce rattling to the top so I'd suggest to use the 22m5 Version.

5 Holes fitting d6/ d10/ d100 (max 16mm; 17mm+rounded corners)

• fits d8 as well if higher, original cover is used.
  4 Holes fitting 2d4 each or 1 of any other.
  3 Holes fitting all but D6 > 15mm (up to ~19mm diameter)

Example-Combinations:
2d4 + 5d6 + 1d8 + 2d10/100 + 1d12 + 2d20
8d4 + 2d6 + 1d8 + 3d10/100 + 1d12 + 1d20
4d4 + 4d6 + 2d8 + 1d10/100 + 1d12 + 2d20
2d4 + 8d6 + 1d8 + 1d10/100 + ------- + 1d20
2d4 + 7d6 + 1d8 + 1d10/100 + 1d12 + 1d20
2d4 + 1d6 + 1d8 + 7d10/100 + 1d12 + 1d20

replace d6 by d8 with original lid

I printed mine with Eryone tri-color Silk PLA on a structured buildplate to get this look.

Thanks again to the original designer (see link / remix note below) !