Cockatrices appear to be spawning in any light level. Furthermore, they don't seem to de-aggro unless if they can't get to you.

I also haven't seen any Aechor plants yet, but I haven't been far from my house.

This might be fixed idk I haven't checked yet.

This still occurs, however seems to be caused by some issues with the Eternal Day system not making the Aether be considered day when its night in the overworld.

Yeah. Since it looks like it's just a daytime sky overlaid on top the normal. You get a similar issue with shaders where you can see past the Aether's skybox and see what time it actually is. Is it not possible to make time stop in just one dimension?