@TD-er for a start I ran the same binary DOUT lib-eeprom read/write sketch on esp8285(1M) and esp8266(4M) with good results.

#include <EEPROM.h>#if AUTOFLASHSIZEvoid flashinit(){  FLASHMAPCONFIG(FLASH_MAP_MAX_FS); // maximum for FS  // or FLASH_MAP_OTA_FS (maximum space for OTA, rest of free space for FS)  // or FLASH_MAP_NO_FS (no FS needed)}#endifvoid setup() {  Serial.begin(115200);  Serial.printf("\n\nsize=%d\nsize=%d\naddr=0x%08x\n\n", ESP.getFlashChipSize(), ESP.getFlashChipRealSize(), EEPROM_start);  EEPROM.begin(512);  Serial.printf("%02x %02x %02x %02x\nwait 10s\n",                EEPROM.read(0),                EEPROM.read(1),                EEPROM.read(2),                EEPROM.read(3));  delay(10000);  Serial.printf("write\n");  EEPROM.write(0, 0xde);  EEPROM.write(1, 0xad);  EEPROM.write(2, 0xbe);  EEPROM.write(3, 0xef);  EEPROM.commit();}void loop() {}

esp8285:

size=1048576size=1048576addr=0x402fb000

esp8266:

size=4194304size=4194304addr=0x405fb000

So, you've already started with it :)
The earliest test I can do with it is tomorrow evening. (I also have 2M modules)
Have got to finish something else now and will be away most of tomorrow.

I have not yet tested it, but looked through the code.
TheflashInit function is called from the core main function and does look at the flash size to pick a layout.
Can I later set it again to another layout at runtime?
Or is it possible to set the magic byte to define some alternate setting and then reboot to load the alternate setting?

The reason I'm asking is that I cannot support a single binary for 4M flash with either 1 MB SPIFFS (default for all nodes out there running my software) or 2 MB SPIFFS if it is only looking at the flash size.
So either I have to have my own detection algorithm to see where the SPIFFS is located and change at runtime, or only try once to find any existing 1M SPIFFS and if it isn't there switch it to the 4M2M option, write that to the magic byte and reboot.
If it still cannot find a valid SPIFFS, then format it as a 2M SPIFFS.,

N.B. the reason I have not tested it yet, is mainly because of the amount of work needed to get a PR ready within PlatformIO. I also just made a feature request for it:platformio/platformio-core#3239
In the retrieved packages directory of PIO, the git config is not complete or correct.
I do see the pull requests on origin, but when I want to checkout based on a PR, I get an error like "missing delta bases"

The flashInit function is called from the core main function and does look at the flash size to pick a layout.

That is on purpose.
The parameter (what you call layout) is in fact an array of layouts indexed by the flash chip size.
There are three hardcoded layout sets, but you can use a self-defined one.

Can I later set it again to another layout at runtime?

FSes and EEPROM should be closed before doing that, but yes I don't see any reason against that.

As@earlephilhower said elsewhere, we cannot autodetect SPIFFS because there is no signature. I don't know about LittleFS.
In either case the information about location and size can anyway be written somewhere and allow to build the right descriptor.

For my own purpose, I could also use the EPROM part to store something with a very specific signature to help detect the used offset.
It does probably have 2 possible locations at most for any given flash size.

this file contains all the addresses computed by boards.txt.py.
I think the easier path is to use the example provided in OP then change FS addresses:

... (later)close_all_FSes(); // or notFS_start = myFS_start;FS_stop = myFS_end;SPIFFS.begin()...