I think you're reading too much into that comment. Putting a wheel file directly on sys.path is no different from putting any other zipfile directly on sys.path - whether or not it will work depends on the context, but it's a useful capability if used responsibly (as we do in the ensurepip implementation).

The key problems with eggs in relation to this were:
- easy_install preferring to install as eggs by default
- setuptools install a global site hook that added every installed egg to sys.path for every application run in that Python installation

Neither of those applies to wheels - pip always unpacks them when installing, and if you want to add one to sys.path you have to do it manually, it doesn't happen automatically.

All the new note in the PEP is clarifying is that it *isn't* an accident that the wheel format is zipimport compatible for pure Python wheels, we deliberately designed it that way (hence the "Root-is-purelib" setting, rather than requiring separate purelib and platlib subdirectories).

Cheers,
Nick.