The shell isn't digested, but the skin of the puffer is such that it stretches as per requirement and doesn't get any scratches or cuts.
One thing you might want to remember when including other fish along with a mbu is, no hyperactive feeders such as dawkinsia barbs, I have noticed that when the mbu poops, these barbs try to eat the poop, and in the process keep pushing the poop back in and the mbu gets really stressed out.(I know it's gross, but this can eventually kill the mbu)
I feed it mostly crabs and macrobrachium shrimps and a few species of snails as apple snails, ramshorn snails, malaysian trumpet snails, and two indigenous species I collected.
Crabs and macrobrachium shrimp come from the wild, so they are frozen for a few days before thawed out and fed. Thus killing any parasites that might be present.