Hi Vaughan,
Your choral score is beautiful, Most impressive. Well done. Another fantastic use of lilypond.
It seems your score has become a standard benchmark for lilypond performance tests now!
A couple of points. It is very often the case that when running Linux on Virtualbox or similar under Windows or Mac OS X that the performance, both disk IO and CPU, even though on the same machine, is better. While I have never looked into this deeply, it is readily observed. I am not convinced that it is due to the design of UNIX because Mac is essentially UNIX under the hood as well. On my Windows 10 machine your score compiles in about 55s and on Linux in a VM on the same machine about 35s. Others here have similar figures.
Also, you mentioned you use MIDI for score checking. You could separate the midi generation and the PDF generation. Run the midi when you need it, and generate the PDF score normally. This would speed up your workflow a lot. You could even have a small script that kicks off both compiles in parallel at the same time. I am sure it does not matter of the midi finishes later [I think it is the midi that takes the time?]. Just an idea.
Andrew