The system was wiped, which was intentional, but it was, unfortunately, upgraded to Ventura in the process.
This is why I had to re-install everything from scratch, layouts included.
The last time I installed them I managed to remove the default keyboard layout, and use a custom one instead.
Now, I cannot. It might be due to Ventura, maybe there are other reasons for this behaviour.
I copied my old layouts which are saved in an external drive, however when I install them, I cannot remove the default layout, even though I don't need it.
To the best of my understanding Mac requires at least one latin layout, but even though the custom layout that I defined and installed is English - Latin, I still cannot install it as the ONLY layout.
This is the essence of the problem, I tried to simplify it as much as I can. I imagined it was due to Ventura, since that sounds like the most reasonable explanation.