It will explain it in time, remember that the books don't end with the end of the war. There's an aftermath section that gives a better sense of closure and buildup towards F/SN.
But for this epsisode... Ah, the subtle beauties of these scenes in motion. Rider's final charge, filled with satisfaction, punctuated by force, and ended only by Gilgamesh's very last resort, Enkidu's chains. If I recall correctly, the books describe Rider's charge symbolically, as well. In his mind, Rider was running on the beach of Oceanus, excited and overjoyed like a child, surge of waves in the background, at the same time as he ran forward across the bridge. It gave sort of a duality to the statements "have you awakened from your dream?" and "the sound of Oceanus' waves was my own heart".
Something I felt noteworthy that was difficult to communicate visually, Gilgamesh and Iskander held the greatest of respect for each other. Gilgamesh doesn't draw Ea for just anybody, and to jump immediately to using it to break his Reality Marble was an absolute sign of respect. Gil's usual MO is to just throw noble phantasms at a problem until it goes away, and some problems are beneath even that. (Recall Gil's disgust at Caster's abomination) Waver's survival in the end came down to this respect. Gilgamesh did not spare Waver out of respect for Waver's devotion, but out of respect for the fallen Iskander's order to live.
And with that, Waver has become a man capable of returning the gaze of the King of Heroes himself. He came looking for the respect of his peers and betters in the magician's society... he leaves with something far better... the respect and friendship of his King. Waver goes on to become the next Lord El Melloi, replacing the now deceased Kayneth, proving his theories right with his new found self-confidence. Watch for him in the Kaleidoliner anime! He comes to Fuyuki to clean up after Rin and company when they bork things up since there's no church supervisor for what passes for Kaleidoliner's holy grail war. XD
On the other side of Fuyuki... Saber is lost in a pit of despair. Her most trusted knight raises his sword against her in blind rage, and triggers every last self-doubt she had about her reign. We may see more on this, we may not, so I'll sort of hold off on the Saber vs Berserker fill in until I know which way that's going.
Also. Kariya, just die already. You're more of a cockroach than the bugs you control.