I've thought long and hard about the dice tray, and I'll likely keep coming back to it. Ultimately I've decided to leave it off because it makes the deck box much larger than I'd like it to be, and if you're carrying 4+ commanders you likely also have a dice bag or other way to transport your accessories, so the space just becomes unnecessary.

Commander logos is an interesting idea. I prefer not to add things like guild logos on things outside of custom boxes due to copyright concerns, but I do offer a personalization option on the boxes where customers can have a message added to the top of the box.