I really like this idea, especially as it means DF might get multithreading in the areas it needs it most, but there's one potential show stopper (which isn't so much an issue with the openGL code):
Even if the pathfinding and fluid simulation were as modular and abstracted from the rest of the game as realistically possible, toady will in all likelihood have to modify the code later if there's some major map structural change (especially on a similar level of 2D -> 3D).
The openGL code for the 40d## series more or less doesn't need a massive amount of touching as long as toady doesn't port DF to the crytek engine (best kitten smashing game meets the best korean smashing engine), so it might as well be magic, but if the fluid and pathfinding were rewritten using the best intelligent caching systems and multithreaded to scale indefinitely to 2, 4, 8 or even 512 cores, toady would need to fully understand it to continue to develop DF with any kind of independence.
(By the way, I do realise the horribly condescending tone this post has in regards to toady "understanding" things, but he's stated before he doesn't have a particularly good grasp of multithreading (nor is he particularly interested in improving said grasp), so I think it's a fair point.)