@luz Do you have any example of software SPI? I try to use GPIOs but I get an error (I don't have the exact error as I'm at work, but it's someting like can't find spi-gpio-custom, maybe it is a external module).
I have an omega2+ and I'm porting Mbed RA8875 drivers from a STM32F401 using SPI.
"Warning: Connecting a signal to an input pin below the minimum LOW or above the maximum HIGH voltages may damage your Omega!
Standard 5V logic devices typically accept 3.3V as a logical HIGH, however, they output logical HIGH in the range of 4.4V to 5V. This means that the Omega can output to a 5V logical device, but input from the 5V logic device would damage the GPIO input circuitry."
With the /overlay having almost the same size as /rom, I would guess something in the update/reset process has duplicated most of the firmware into the overlay, for some reason, instead of completely emptying it.
I would have a look into /overlay, that's where you can see the files which occupy those 7.3M.