The auxilary plugs in the photograph are used to connect the wires from the auxiliary power outlets, which are located on both sides of the digital dashboard.
Another two power outlets, A1 and A2, will be located under the saddle. These auxiliary power outlets will be controlled by the switch on the right handlebar, under the engine kill switch.
When the switch is set to '0,' both of the power outlets under the saddle are turned off. When the switch is set to 'A1,' the A1 outlet will have power. When the switch is set to 'A2,' the A2 outlet will have power.
Most battery tenders for motorcycles come equipped with a 2-wire, SAE plug which connects directly to the battery terminals. After connecting this wire to the battery, you tuck the pigtail connector on the other end into some convenient, accessible spot on the motorcycle. You can then connect the battery tender to the battery with a similar SAE connector without removing the saddle, or you can remove the saddle and use the supplied jumper cables.
Therefore, I suggest you don't remove either of the auxiliary power connectors on the wiring harness.
Leave them in place for the optional power outlets on the dashboard, or for some other future accessory.