That tutorial is difficult to understand without the pictures, but from what I gather, it's a way to specifically edit each palette in the lightmap instead of editing them all at once with Uberlightmap Tool.
I don't think it's a ltmp problem. The lightmap seems to apply to the BSP and things in contact with it (it looks perfect when I'm on the BSP). I think there is some default setting about blocs or models that determines how they reflect light or light up the things in contact with them.
For example, here I am not touching the blue base gate.
Now touching the blue base gate. It gives the biped a bluish light, independent of the lightmap.
I think this is the key. It's the cause of the old green mach problems, these reflexives with pointers that don't point to anything when you build the mach into another map. The blue and red base gates have settings to indicate that they give off a blue or red glow to objects that touch them. I need to figure out how to adjust what color the light is, and put those chunks on my bloc models.
I think neodos is the only active researcher who can figure it out though...
EDIT:
How did T Beezie get this yellow lighting effect from the gondolas? This was almost 2 years ago.
His lightmap looks really funky, too:

Retired. Thank you neodos, DemonicSandwich, DarkShallFall, Dragonfire, foxfanatic2317, GOWO and everyone in the hall of fame.
If you want to know how I did something, take apart my mods.