You will have two UVW Map channels. The first one is for your textures/materials, the second is for lightmass.
You are correct about the UVW map for your textures. They can be anything you want it to be, just like in Blender. All it does it determine how your material will lay on your geometry, as you sound like you know.
The second UVW map channel is the one for lightmass. UE4 basically bakes the lighting and shadow information into this map channel. If you have over lapping UVWs or UVWs that are messy, UE4 doesn’t know what to do with it. That’s why everything needs to be mapped out correctly in this channel. This is a pretty good article that helped me wrap my head around it when I first started: http://www.worldofleveldesign.com/categories/udk/udk-lightmaps-01-basics-and-important-principles-for-creating-using-lightmaps.php
I highly recommend learning how lightmass works and how to properly unwrap your UVWs. It can be a pain in the butt at first, but if you take a week to learn it you will never have a problem again, and as you can see by looking at this forums a LOT of the problems people have are caused from not understanding this process.
I hope this was clear, please don’t hesitate to ask more questions. I have a similar background as you so I’m can relate to what you’re experiencing.