I have never cared about this.
But, if there is such warning, maybe someone had have some mistake in the past. Or maybe, because you end up with a lot of carbage in /opr/freescale/pkgs.
I have never had problem with it, but I always used Ubuntu.
You can try to change the ltib file (file is called ltib, it's a script you can edit) in order to have a different /opt/freescale/pkgs
There is a lot of files inside /opt/freescale/pkgs. If bsp 11.09 uses (i.e) alsa-1.10 and bsp uses alsa-1.9 you will end up with both, but your ltib will only take that one it needs.