Say I have a large area shaped like a 'T' and want to (for example) make it very dark when the player enters a trigger box formed around the T. Since trigger boxes are square I would have to make two boxes, one for the T's stem and one for the top.

Is there a way to link those two trigger boxes together so there is no break (in the darkness) when the player moves from the stem to the top of the T?

While I'm not sure exactly how you have it set up, I'll assume you have a straight hallway, which at the end has a three way piece with hallways extending outwards, forming a T (pretty big assumption I'm making, I know!). Instead of having a trigger covering the entire hallway setup, why not have three smaller triggers at the edges of where the effect would turn on/off. They could check to see if the effect is enabled (whether it be through a global, a quest, whatever), and if not, they turn it on. If it is on, they turn it off.

Of course this wouldn't really work in an exterior space where you could probably just jump over the triggers, but if it's an interior or an enclosed space in the exterior, it should work.

EDIT: Ah, didn't realize you were the author of Real Shelter. I'm guessing that since it's likely in the Tamriel space, it won't work.