Basically, if you put a maze generator in a structure (1), set it to spawn the maze, and spawn structure 1 within another structure (2), the maze will be spawned as if the maze spawner (script block) was in structure 2, at the same distance from the block at lowest x/y/z thta it was in structure 1. For example, I can't link the srtucture as it requires many mods, but I put a tower, which generates a bridge from its top, which leads to a floating island (3 separate structures) with the maze in it; the maze will be spawned in the tower.

I'll add some screenshots to make this more understandable:
How it's supposed to gen
This is in the structure normally spawned through a list, when spawned with /#gen. Notice the little maze entrance: the maze is exactly where it has to be.
How it generates
The mushroom-tower-thingy leads to a bridge, through TC levitators, that leads to the island (previous structure), and you can see in the bottom of the picture that the maze generated in the bottom of the tower.