From the Espressif datasheet for this module, here are the pin groups you asked for:

These are the module strapping pins used at reset:

What they control:

That is the only pin in the module pin table marked input-only.

There are two useful interpretations here:

These pins are labeled with FSPI/SPIIO functions in the module pin table:

The ESP32-S2 chip datasheet says the pins allocated for communication with in-package flash/PSRAM should not be used for other purposes. On the chip, these are the dedicated SPI memory pins such as:

On the module, the always-reserved internal flash connections are generally internalized rather than simply exposed as ordinary user pins, so if your goal is a safe "do not use casually" list, the cautious exposed-pin set is:

If you want, I can also turn this into a clean Flux terminal classification table with columns like Pin Name / Pin Number / Pin Type / Section / Pin Group / Notes for your part project.