OK, I checked the differences between the theatrical and SE versions and it seems that the broadcast was the SE version after all and the DVD upscale shots were probably used to replace some scenes damaged or missing in the HDTV capture - there are some glitches here and there, the kind you get when you have a bad signal on a digital broadcast, so I can imagine that if some scenes were riddled much more with those, the creator of this encode decided to replace them with the DVD, although the DVD upscales look pretty horrible (though still better than the PAL DVD, so I assume that the NTSC DVD does indeed look better).

As to the movie itself, I found the first half pretty boring but then it picked up. Maybe I'd actually like the theatrical version better, but then I liked the scene where he's aboard the Alien ship at the end and most of that is apparently an SE addition.