I've learned a lot from the clipping discussions here and in the other thread, and banging around in the source, but I don't have much to contribute toward improving the solution.
What I can provide is bsp2 and 2bsp support. That was the mystery of gigantic maps... really just a file format. So far the bsp2 scenes have not broken software limitations on rendering frames. This is based on MH's notes and the quakespasm implementation, which very elegantly laid it out. I'm not ready to put forth a build yet but the code is on the sourceforge svn.
The bsp2 format is layered on the 'big map' format which is actually more complex, many data size changes and limit increases all over the place.
Here's one of the worst cases I could find of the single-pass transparency option: the green arrow shows missing slime through the grate, the red arrow shows missing grate (and slime).
