Modules are really about environments (including software management). Anaconda doesn't handle this. For example, Conda its version of HDF5 and points to its environment path. Let's say you want to be using a different version of HDF5. An easy way to do this is just use a module so that you load this. You are creating an easy way for the user to set up their environment, where they really don't have to know anything about it.
It also helps with versioning. It is not uncommon to see various versions of gcc and intel compilers. In essence the user should be able to load their environment with a few module loads.