People say this story is a tragedy, but I honestly don't think it is at all.
The role of a Beholder is to care for and stay by the God. That's why Taro believed that although he was made for Tomoya, Tomoya would never become his. However in the end, Tomoya gives Taro his gem (a representation of his Godliness). By keeping this gem, Tomoya symbolically gave himself to Taro just as Taro has done for him. If this story were really about acceptance and forgiveness, why have Taro keep the gem? If he had really forgiven Tomoya and accepted his descent, he would have given the gem up. It's also seen in the extra that Tomoya still stays by Taro's side. So, what if in their relationship the Beholder and the God belonged to each other?
I know I may be pulling at strings, but I hope my analysis may have helped you wipe a few tears.