There aren't really any downsides to letting SnapDrive do it automatically.
The ability to do manual igroup management was added for people that want to be able to specify particular igroup names, etc... .
The unique LUN IDs is not really a SnapDrive "issue" but storage system topic. On an active/active (or clustered) storage system, the LUNs IDs do have to be unique since the LUNs are available across the ports on both controllers with the same WWNodeName across controllers. When mapping LUNs the storage system checks if the number (the N in LUN) is already used for that igroup and only allows unused numbers.
Cheers,
Rick
