it SHOULD be in hl2, if they had it on tf2. hard to say if they did, though, because all we ever saw of tf2 was a bunch of non-gameplay scripted sequences.
it is interesting that his third arm looks stitched on. but i think the real reason it is that way is because the folks at valve thought it looked cool...
you guys read way too much into little details.
i have a feeling valve is doing something pretty interesting, with at least 3 or 4 factions... isnt there supposed to be a different group or rebels being led by a different scientist?