The ESP32-S3 has two USB controllers; one is the Serial/JTAG one you've been seeing and the other is a USB OTG controller: https://docs.espressif.com/projects/esp-iot-solution/en/latest/usb/usb_overview/usb_phy.html
I think you will need to switch USB controllers in your build.
at the start of ports/esp32/main.c' s mp_task(): we have this:

void mp_task(void *pvParameter) {
    volatile uint32_t sp = (uint32_t)esp_cpu_get_sp();
    #if MICROPY_PY_THREAD
    mp_thread_init(pxTaskGetStackStart(NULL), MICROPY_TASK_STACK_SIZE / sizeof(uintptr_t));
    #endif
    #if MICROPY_HW_ESP_USB_SERIAL_JTAG
    usb_serial_jtag_init();
    #elif MICROPY_HW_ENABLE_USBDEV
    usb_init();
    #endif
    #if MICROPY_HW_ENABLE_UART_REPL
    uart_stdout_init();
    #endif
    machine_init();

I think in your mpconfigboard.h file you will want to #define MICROPY_HW_ENABLE_USBDEV (1) and #define MICROPY_HW_ESP_USB_SERIAL_JTAG (0). It looks like the ARDUINO_NANO_ESP32 is the only board that has this defined so far.

See the issue I raised at #17672 also the discussion at #17633.