I think it's more than just that. They just randomly played it 3 times in a span of a week in 2001, and never played it again. It's not like they played it for an entire tour, and it wasn't at the beginning of the tour that they played it either - there's no way they came up with it during rehearsals, so it must have been something they knew beforehand. The drums, guitar, and bass all flow together perfectly, and LP wasn't an improvisational band in the slightest in 2001, so it's HIGHLY unlikely they came up with it on the spot. It's probably part of an old, unreleased song, possibly even Pictureboard. It could also be some random Xero/Hybrid Theory song or a Hybrid Theory album b-side that we've never heard about.
There's also the slight possibility of it being an obscure cover song. Brad, Phoenix, and Rob all obviously knew what they were playing, but Joe and Chester just improvised over it.