Files are just a collection of bytes.
If you want flashing tools to manage this you'll need to translate the data to a .HEX, or rename/copy to a .BIN
You'll need to decide the address you want this data to reside.
On the program side you could facilitate the writing of data to a designated area of flash.
The reading would be done like any other memory access, you can use pointers and structures, and you can inspect memory to see if it is erased vs containing configuration data.
