I think mostly due to clearance type issues... but also a root style blower replaces the intake manifold correct (or am i off here? I'm not the most knowledeable person on FI applications)
So if that's the case a big problem is the fact that the LS6 and LSX intake manifolds are already flowing very well... and w/the LSX intake manifold (and holley LS6 style) you can port match the intake manifold ports to the intake ports on the heads ... can you port the supercharger intake outlets to match the heads?
Also aren't roots style chargers less efficient ? (this i really dont' know about)
Just seems like w/the LS1s I always see the non Root style (not sure what that's called?)
Good question though... maybe some of the FI guys here can give a better answer