1) You can disable that if you dont allow ssh access.
2) This is useful for multiserver mirror setups as it ensures that the web users on all mirrored servers get the same linus uid.
3) That can be useful on customized installations which use a different folder scheme and / or external storages.
Last but not least, Enable SNI. The hint in the manual says, that this is only needed if I want to run multiple SSL on the same IP. So if I don't plan to do this, can I safely deactivate it?