Minecraft will crash if you attempt to create a superflat world while the default LC preset has the option to always spawn the player within a LC enabled. Likely just checking to be sure a world is not superflat before running any such code would be enough to fix it.

one day

Supperflat isn't supported by Lost Cities and is also not really possible the way it works

Would it be possible to have a config option that disables the LC worldgen if a superflat world is attempted to be generated?

Supperflat isn't supported by Lost Cities and is also not really possible the way it works

Can it just disable or run the disabled preset when one is generated to allow making a superflat without removing the mod to do so?

I may be able to do that but I don't know how and this is also low priority. I have way too much other work with my mods right now