So GPIO performance won't be a problem, but they note that OS multitasking can cause issues:
"What is not evident from the snapshots, however, is that due to multitasking nature of Linux, the GPIO manipulation is constantly interrupted for short periods when the CPU is doing something else, such as receiving or sending data over network, writing log files, etc"
Running on bare metal should take care of that, so the only remaining problem is how to synchronize the signal generation on the RPi with the recording of data on the host computer. (Sigh, if only RPi had a USB3 port...)