Never???
Win 3.x (I don't know about earlier, because didn't use them) has some shells, different of standard. The most popular was made by !Symantec!
And shell= string in the Win95' system.ini is the direct legacy of them.
Yeah, explorer became a part of the system - it was associated with folders, iexplore use it and explorer use iexplore...
but it isn't full integration as you think, and in Win 3.x it wasn't too...
Don't say 'never'...