As far as I know, "The Gathering" has only been presented in 4:3, including the re-edited version you are seeing. Have you tried playing it using another media player or on a television?
When sci-fi showed it, they did show it cropped to fake widescreen.
Here's the deal with that one ... Warners did a set of roughly 10 pilots, which they released for $5 each (I believe that was the price). Friends was another one that I recall seeing. They came in a thin cardboard case with a coupon that could be used for $5 off the purchase price of the first season of that same series. It was a promotional tool, nothing else.
There were complaints at the time that the pilots shown that way had been edited (or had the syndicated version, perhaps?) and were not the version of the same pilot on their box sets.
What they probably did was take that sci-fi file, put it on DVD (since there were no extras; I don't even know if it had a menu or if it was auto-play) and mass-produced it very cheaply without spending anything to clean it up in any way.