I actually found this about a month ago but I haven't seen this mentioned elsewhere so I might just as well paste it here.
Lameduke has intermission screens between levels, you actually need to disable the developer mode in game to get these.
While many have seen these at some point, the EP1 and EP2 screens actually blend together seamlessly!
This makes me wonder if they intended for the screen to scroll between episodes or during the episode itself.
While the level order is very WIP obviously, this screen could tie in the sudden shift from space levels to the city levels during EP1.
(For reference, I made a annotated playtrough recently of the whole game in
HERE, Similar to the 0.99 comparison I did).
Looking at the ingame level screenshots, U.S. bank tower is visible in the intermission screen along with being present in E1L6-8.
It's getting clear however that after space they had planned a trip to L.A. , My theory is that E1 was to be fully in space and E2 would be as-is until L4's end (Random streets of L.A.) as it seems to end in a location that would take you to E1L5's subway. This would make the most sense as the first half of E2 is in L.A as is the second half of E1.
After this a more coherent story exists:
EP1 Starts where DN2 left off, in a space station.
EP2 Duke teleports in to L.A. from space. (End of EP1 is rather vague)
EP3 Duke is captured(?), Takes a ship ride to some rocky underwater base.
EP4 Unrelated ,just two tech demos/testmaps & one DM map.
Although, a lot of this will probably be a lot more clear once the missing beta builds get released eventually