I don't think the pilot was ever a two-parter, but I also don't remember seeing it that often, if ever, in syndication. The episode - The Menagerie - that reused lots of material from The Cage, was broadcast as a two-parter.
The Cage was first released to video around 1986, and the remastering was probably at the same time (2008-2009?) as the rest of the first series. Stations also broadcast the remastered episodes in syndication at that time, so that was probably the first time The Cage was broadcast outside of some anniversary commemorations.