So, it seems that even though I have:
mods.DimensionStages.addDimensionStage("a", 4);

I can walk through the portal to the Aether without having that stage.

This is an issue with Aether Legacy, they are not firing the forge event like they should. Please report this issue to them. Could you please include a reference to this issue, and this code. Those two things should help make it much easier for them to fix it.

Yeah, I figured it was on their side.

Ok, they fixed it in the latest version.