I just realized bits 7 and 8 being set to 1 is illegal for 8253 but not 8254! Maybe I can work on implementing this "read back" functionality.

The error is misleading. They're not using the PC speaker at all. They are accessing the timer in an illegal way for benchmarking purposes. I'm currently investigating into this further. (guestimation follows) Basically they output E8h to port 43h upon launch and expect values back before they send …