As of the time I had posted this question, I have found a answer:
I had used a dropper for my custom crafting device. Droppers are non-transparent blocks, and there is no way (That I know of) to change that without modding.
Chests, however, are not, and can be used as the custom crafting device. Placing a chest in place of the dropper (Or other block you use) also allows you more freedom for custom blocks that have uses.
In conclusion: Although slightly more confusing to work with, chests are a better option for all of your custom, functional block uses.
