No difference at all, it just means the status of the gateway is not visible to other users querying the status endpoint.
These settings do matter. If you have a gateway running the old Semtech packet forwarder that gateway will not buffer downlink packets. Any new packet that is sent to the gateway will replace any packet pending transmission. By setting the late option you ask the back-end to transmit the downlink at the latest possible moment minimizing the chance of it being replaced by another downlink.
The time delay allows you to tune the setting, this might be required for network links with high latency to make sure the packet arrives in time for transmission.
These settings are only applicable for the TTN Kickstarter gateway and gateways running Basic Station. The updates concern firmware as far as I know and will automatically be deployed when the gateway checks in (at least once a day). The channel is where you specify information on where the firmware should be obtained. May-be someone from the core team can provide the details in this?