The LS6 version allows more airflow due to increased depth of intake.
Notice how flat and even the LS bottom is compared to the older LS1 version.
To allow the existing cooling lines to be maintained the shallow ridges were ground down for proper clearance
If you look at the older LS1 version you can see that bottom had ridges for the cooling lines but the LS6 version did away wth those ridges to allow for a deeper air passage which increases airflow, thus more performance gain with proper head and cam changes
The following /image allows you to see those cooling lines, via the 1/8th inch tubing running from one head to the other.
Important is that you properly torque the bolts down in the following order using Nm or inches
Once installed, it now looks like this: