Your new sky box only exists on the logical client:

src/main/java/com/example/structure/sky/EndSkyHandler.java

Which has the annotation:

@SideOnly(Side.CLIENT)

This is resulting in a crash on servers when a player enters the End dimension, as this class is being invoked on the server-side, where it does not exist, and so throwing a Null Exception:

The solution is that this EndSkyHandler should not be annotated as Client-Only. These IRenderHandlers are present on both client and server. The bit that needs to be Client-only is only the getter for it (which you have annotated properly).

While I'm here.... your mod code here on GitHub is not the same as your latest release for servers on Curseforge. This means I am unable to offer a Pull Request or fix this on my side at all. Please update your GitHub repository! Without that I can only bin your mod, not fix it - we're in mid server-play and we have not much option to either bin your mod or get an immediate fix :(

Fixed in 1.0. Please let us know if anymore issues occur. Thank you!