You may wish to avoid installing into the user home directory; for example, it may be on a slow volume.
Using a directory such as this for preference, log, and other files that are disposable (though at a cost) is a fairly standard practice. This is particularly crucial when the main software is installed in a directory which is not normally writable.
Canopy uses a multi-layered virtual environment, which is described here:
If you wish to relocate the User and System virtual environment directories, you may do so by quitting Canopy, editing ~/.canopy/locations.cfg in the obvious way, removing ~/Enthought (to be tidy), and restarting Canopy.