The difference is simple: He plays different keyboards in Vid 1 and Vid 2! Vid 1 is what looks like a vintage organ plus what looks like some analog monophonic synth (but might be a shortened keyboard for other purposes, I'm no keyboard expert), Vid 2 has some modern day digital synth trying to emulate those sounds. And that is what you hear: an emulation, ok on its own, but when compared to the original sounds it has none of the depth, warmth and oohmph. To be fair: Vid 2 is seven years earlier, we all know how much digital sounds can improve, that's at least two keyboard generations. So it's probably fair to assume that a digital reproduction of Manzarek's organ (the one with the keys!) would have sounded quite a bit better in 2000 than it did it in 1993. A lot happened in the intervening years. When the DX7 came out, I thought it was the most amazing thing, a couple of years later those orignal DX7 sounds appeared kind of naff, we were all spoiled along the way by sonic improvements.
But in the end it's what Jon Lord said about digital Hammond emulations: "They sound so much better today than they used to. But only as long as you don't play them side by side with the real thing."