All of this may sound cool.. but you need to remember that the goby and pistol shrimp pairing up is one of those hit or miss things. It won't always happen, but it is possible. Don't be disappointing if you get the two expecting them to pair up and they don't..
Also.. i haven't seen a single goby that wasnt reef safe. All of them are.. so don't think that having coral will limit you as to what kind of goby you can get.. So far... every single goby that i have seen for sale on multiple sites.. are all reef safe.
For the pistol shrimp, you don't NEED to set up your tank with eggcrate or anything.. you just need to make sure that your formation is totally secured. The rocks at the bottom of the structure should be placed firmly in the sand, or touching the bottom. If a rock were to fall.. it would fall on the sand bed.. and wouldn't even come close to the glass on the bottom. And i know this because you will at least need 3" of depth in your sandbed if you want a pistol shrimp. They need that depth to burrow..
I have a 2.5" sandbed depth, and i have dropped a good size rock all the way from the very top of my tank, all the way to the sandbed.. and it didn't even get half an inch through the sand. As long as your structure and your bottom rocks are firmly secured.. you will be fine.