Right now, the mod preset and the launch parameters are independent of each other, i.e. the parameters are not saved along with the mod presets. Switching the mod preset will leave the parameters as they are.
It would be very useful to be able to e.g. have a "Debug" or "Develop" config that has showScriptErrors enabled, while a normal "play" configuration would not have it on.
Likewise, it would be advantageous to be able to have a mod preset for different servers with different profiles, direct connection to a server, etc...