You have to remember that just because the Tribunal are gods at the time and couldn't be killed, their people could still have suffered massive casualties at the hands of the Red Empire. The war was already long and bloody at the time the treaty was signed - they'd seen enough bloodshed.
Also, as has been stated, the Tribunal or at least Vivec recognized Talos for who and what he really was, and made way.
No, that's wrong. The war with Reman was long and bloody, lasted for 80 years, and the dunmer suffered heavy casualties. Morrowind eventually lost, and was then invaded by Mehrunes Dagon shortly after.
With Tiber Septim, not a single drop of blood was spilled. Tiber was ready to make war and amassed his troops all over the northern, and western borders, and the dunmer were all prepared, though Redoran would be the only fighting force toward the west, with Indoril and Dres in Vvardenfall. However, Vivec appeared in Vivec City. Vivec and Tiber met, negotiated, and an armistice was declared and treaties were signed and not a single person died. Well, except for a lot of the Indoril nobility that committed suicide shortly after the treaty.