So looking at the overworld and farmworld, they can mostly be considered the same except for the fact that "structures" like AE meteors, Thaumcraft obelisks, and those extensive dungeon structures from that one mod i don't remember. Can anyone tell me why these are left out?
Many of those structures are only set to spawn in the over world. Theye do not spawn in the Farm world because while it is over world like, it is not the overworld.
Wouldn't the very simple solution be to generate a overworld with the structures and paste the map onto the farmworld.
Nope. Because some things are generated in that expect to be in the overworld. Thaumcraft portals, and end portals come instantly to mind.
Taking that into mind you could have a warning made put into the lore of the EYE stating that you will spawn in an endless void and to be prepared. This is already an issue if you craft the craftable portal to the Eldritch dimension (falling into endless void) and for the end portal just remove the end frame from the generation config or whatever. This would allow people to find crimson cultists and Rouge Dungeons without having them be destroyed already.
The eye is doable, the frames, harder then you might think. I know that they are looking into different ways to generate farm worlds in 1.10 and beyond, but for 1.7 I doubt things will change.