Shuttles have a greater structure that is difficult to manipulate... You essentially get what you have, and can only add to it. Due to the fact that they are designed to carry "passengers". (DOT safety, which also shows when you have to register it.) They are heavy, hard to insulate and best when parked.
Box-trucks types are all over the place... Metal, wood, plastic, fiberglass, cloth... It depends. Most are just fiberglass and metal construction. You will find modification to them to be easy and more like modifying a house and less like modifying a "boat". (As a shuttle-bus is compared to modification, due to all the odd internal curves and irregular surfaces.)
There is another advantage to box-trucks, as they can be "stealth", and that matters. (Stealth in a shuttle-bus is a little difficult and almost fruitless.) Stealth, where it matters most, is in registration and living. You CAN register it as a converted RV, or just as a box-truck, legally. (They do not count permanence of contents within the "cargo vehicle", but they WILL in a shuttle-bus, or it won't matter in a shuttle-bus.)
The two major things to think about is what comfort will you want more? Living comfort or driving comfort. The shuttle-bus will potentially have more driving comfort, but it comes at a high repair cost and limited availability for repairs. The box-truck will be more potentially "living comfortable", if insulated correctly compared to a shuttle-bus. It will also be easier to find people to repair it, and parts to repair it.
Depending on the box-truck, you can get more internal room too. Though most are a little taller than some like. Some are as high, inside, as a shuttle-bus. (Shuttle-buses are not typically tall inside. Most are just adequate for standing, of an average sized person, which limits any potential insulation you may need.)
NOTE: You can make a box-truck a better ride... It is not bad, when it is full of stuff, unless it is overloaded or under-loaded. There are also "comfort ride" box-trucks, which already have similar setups to shuttle-buses.