Box looks awesome - thanks for sharing your design :)
Would it be possible if you share the lid and the divider without the commander shield symbol? That way, it would be much easier to add a custom symbol to the box. I'm thinking about a matching symbol for each deck (maybe the mana icons or the contour of the commander).
Here is my phyrexian mana version of the lid / divider. Sadly I can't upload the remix, as the license of your design doesn't allow it: "Please make sure the source model's license does NOT contain "NoDerivatives" attribute. For example CC-BY-ND, CC-BY-NC-ND, Standard Digital File License are not allowed."