VR bills itself as a dangerous rock band, i.e. one willing to take risks. They should not listen to dorky marketing guys with knocking knee caps.
it is a great song and does honor to the victims. It needs to be on the album.
btw, the video is ok, but there is no need to show the plane striking the building. The same impact can be gained without such a literal, visual symbol.
Maybe they discussed it with victims' relatives groups who felt uncomfortable with VR making money out of it. Might not have been the record companys decision alone. There must be a good reason why its not on the album and was only offered as a free bonus track, lets see if we hear one.
It makes no sense from a marketing point of view for it not to be on the album, unless they've decided to re-release Libertad later with Messages (which at this point might be getting some radio airplay) on it, so people would have to buy it twice. If they do, the record company are assholes.