The two times are because the 45 minute one isn't a "true" speedrun, that is, it's made with several demos (and several runs) put together. While it still attempts to stick with the nature of "one run", the hour-ish one is one demo-recording. That's why there's two.
And I watched the HL2 video

Though I think I'd like to see it again when the game's been out longer, and someone has a super-nice computer that can record it at a higher resolution like the HL1 speedruns.
And about the scripted scenes stuff: I agree to an extent. That is, I do prefer when they can work in the looser, flexible scenes you can watch or ignore.
The Plothole: a home for amateur, inclusive, collaborative stories
http://forums.theplothole.net