I'd rather not. Startup settings can be accessed during the data stage, so it's easy to change prototypes based on settings. A per player setting would be possible, but it requires action during the game (i.e. control.lua), so the settings can be applied whenever the configuration changes. The real problem, though, is that it would take some effort to make it desync-safe in multiplayer mode -- which means storing the settings for every player in the global table.
It can be done, but it takes more time than I can currently spend on this mod. May be later, but no promises! :-)