For the record: the cmake profiling data did help a bit. On macOS it seems that the configure stage does 200+ try_compiles, largely due to SDL2, and each one somehow takes ~2.3 seconds. So that's 460 seconds right there. And regarding the total time, it's actually more like 480 seconds. (I must have misremembered! Or perhaps my laptop is measurably faster when its integrated GPU isn't driving 2 external displays.)
On Windows: 50 try_compiles, about half and half SDL2 and libuv, and each one takes ~1 second.
I don't think either of these try_compile turnaround times is acceptable (what is it doing?! I bet it's like 50 ms on Linux) but the total figure does now feel a bit less mysterious.