That's a bit like determining a ship can only be made of wood, isn't it? A ship needs to float, it needs to be made of buoyant material and it needs to have a sail. If a "sailor" is adjusting the power to a propellor that's turned by an electric motor that's running off a turbine driven by steam from a magical rock, it's not what we define as naval science, is it?
The thing missing here is that it's only a ship for humans. Ships are cultural artifacts. If we said the universe was a ship that was sailing itself, that would be misapplying something we make for nature itself. Independent of human culture, ships are just arrangements of matter. We make particular arrangements meaningful.
Same thing applies to computers and computation. It's only meaningful to use those words for matter we arrange to do certain stuff for us.
Yes, by the time you enumerate all the properties of reality, and call them a "computer", you'll find that this is not a computer in the sense of computer science.