After looking at the qrad3 source, it seems MAX_PATCHES may be unavoidable as going beyond that would exceed the amount of memory that can be referenced by a 32bit integer (2 gigs, if it's signed).
Solution: Make smaller maps.
Or use the -chop options. Or scale the textures up so the lightmaps are smaller. (keep in mind that unseen triggers are also lit, so scaling their textures up to huge values can reduce compile time and avoid MAX_PATCH limits with no visible effect whatsoever).