The noise was clearly related to the EverDrive rather than the console:
- Regular HuCards were quiet.
- The same Turbo EverDrive Pro produced the noise on two different PC Engine consoles.
- Removing the microSD card made the whining disappear.
- Noise was most noticeable during SD card I/O activity.
The original card was an Amazon Basics 256 GB microSDXC, V30/U3.
I replaced it with a PNY Elite 128 GB microSDXC, U1 / Class 10.
Result
The PNY card is significantly quieter.
It is not completely silent: faint digital noise can still be heard during SD I/O when the game/audio output is otherwise silent. However, as soon as normal game sound or music is playing, the interference is effectively inaudible.
So in my setup:
Amazon Basics 256 GB V30/U3 → clearly audible SD-related whine
PNY Elite 128 GB U1 → faint I/O noise only, effectively inaudible during normal use
The microSD card itself can have a substantial effect on audible interference with the Turbo EverDrive Pro. Different cards have different controllers, power-consumption patterns, and current transients, which can couple into the console's analog audio path. A faster or higher-rated SD card is therefore not necessarily better for this application, and not needed anyway from a speed standpoint.