From the Espressif datasheet for this module, here are the pin groups you asked for:
Bootstrap pins
These are the module strapping pins used at reset:
IO0 - module pin 27
IO45 - module pin 26
IO46 - module pin 16
What they control:
IO0 + IO46: boot mode
IO45: VDD_SPI voltage selection
IO46: ROM message printing
Input-only pins
IO46 - module pin 16 - type I
That is the only pin in the module pin table marked input-only.
USB pins
IO19 - module pin 13 - USB_D-
IO20 - module pin 14 - USB_D+
Pins connected to internal memory
There are two useful interpretations here:
1. Exposed module pins with memory-bus-related functions
These pins are labeled with FSPI/SPIIO functions in the module pin table:
IO9 - pin 17 - FSPIHD
IO10 - pin 18 - FSPICS0 / FSPIIO4
IO11 - pin 19 - FSPID / FSPIIO5
IO12 - pin 20 - FSPICLK / FSPIIO6
IO13 - pin 21 - FSPIQ / FSPIIO7
IO14 - pin 22 - FSPIWP / FSPIDQS
IO33 - pin 24 - SPIIO4 / FSPIHD
IO34 - pin 25 - SPIIO5 / FSPICS0
IO35 - pin 28 - SPIIO6 / FSPID
IO36 - pin 29 - SPIIO7 / FSPICLK
IO37 - pin 30 - SPIDQS / FSPIQ
IO38 - pin 31 - FSPIWP
2. Pins actually reserved on the chip side for in-package flash/PSRAM
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:
SPICS0
SPIHD
SPIWP
SPICLK
SPIQ
SPID
and, for wider memory modes, GPIO33-GPIO37
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:
Table
Category
Pins
Definitely strapping-sensitive
IO0, IO45, IO46
USB-fixed by default
IO19, IO20
Memory-related / use with caution
IO33, IO34, IO35, IO36, IO37
Memory-bus alt-function pins also shown in pin table
IO9, IO10, IO11, IO12, IO13, IO14, IO38
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.
Wirelessly connects nets on schematic. Used to organize schematics and separate functional blocks. To wirelessly connect net portals, give them same designator. #portal
Wirelessly connects power nets on schematic. Identical to the net portal, but with a power symbol. Used to organize schematics and separate functional blocks. To wirelessly connect power net portals, give them the same designator. #portal #power