What about GPIO46?, that is also indicated within the S3 Datasheet as being involved with Boot Mode determination.

It would be useful to include details of the compiler tool-chain that you're using for this question.

For example,
* Arduino IDE Version xyz
* Visual Studio Code + PlatformIO Version xyz
* Espressif IDF Version xyz
* Espressif IDE Version xyz with IDF Version xyz

Also, your host computer basics ...

I'm trying to get JTAG/OpenOCD working with an ESP32-WROOM-32 module, and variously Arduino-IDE, ESP32-IDE (/IDF) and VSCode / PlatformIO. I'm developing on an Apple Studio (M1 processor, not x86) - refusing to boot my Windows machine; I've tried a linux machine (x86) but quickly had similar ...

I'm assuming that you understand that the FT2232 USB<>UART bridge device is capable of interfacing to a serial flash device - and that's provisioned on the ESP-PROG board, and typically will be empty? The use of that device is entirely to configure the FT2232 device, and is programmed within the FT ...