You can always give config file (-c) for Hatari with the necessary options:
That's the sad part, I did have my own config files but then I saw how you use the command line for debugging/profiling so I was like "why type hatari -c <path to config file>" when I can just run "hatari-ste.sh" ? So I would really like to stick with the command line.
I'm also curious why this checkbox is even needed? As soon FF is enabled, there's no point of having the keyboard repeat active or is there an use case I'm missing?
Anyway, I guess I'll just patch it in the source code to make it OFF as soon as FF is enabled.