Not quite true -- multiple mods can make changes to the technology tree, so long as they don't conflict with each other. For example, you can run Prehistoric Era Reborn, Enlightenment Era, and Future Worlds all together, although if it's not in the right order the tech tree will appear messed up visually.
I've run into the "starting with the wrong unit" error when working on Future Worlds and, for whatever reason, my Technologies.xml file crashes. It would appear that this means that the game doesn't recognize my units as having a tech requirement, and are thus available at the start of the game. I think the game is programmed to try and give you a starting default melee unit with the highest available combat strength, or something similar (possibly the highest unit ID? I've noticed if Future Worlds crashes, it gives out Biotroopers and not Robot Infantry).
The most likely issue, then, is that another mod has defined a tech that the Enlightenment Era mod also defines, and that causes the technologies xml file for EE to crash, or a similar conflict, resulting in any units it defines being available from the start. The Database log would probably be most helpful in identifying if the xml file was conflicting with something else.