I still roll a theory that first half of EP2 and second half of EP1 used to be one.
That way the "City arc" would start with: L.A. River -> Hydro Power plant -> L.A. Industrial -> Subway towards Downtown -> Climax at the top of U.S. Bank tower
Might just as well link this again for reference
And the intermission screens for EP1 and EP2 Need to disable developer mode in order to get these between levels, what is interesting about this one is that there is some subtle crossfading between the space / L.A. sections, maybe it was meant to scroll ?
But in defense, "Mission cockroach" does imply some sort of an infiltration mission going on but these could just be misleading placeholders.
E2M5 does indeed look like a secret base and it even has some huge water tanks, hinting at a similar theme as L3 - hydro power plant.
And that intermission thing could have scrolled in the middle of an episode if needed.
But enough speculation from me, one thing is for sure, there are a lot of giveaways that first few levels of EP2 are some of the earliest ones out there
Presence of bats, overuse of "white concrete", You can see at least one map specific internal comment if you use /q when launching LD and the subway thing I mentioned already (EP1 has them all functioning)
Whatever is present in here will probably explain quite a few things about LD