Right, the way missions are loaded is still somewhat of a mystery to me.. missions from mods get added to the existing list, unlike other lists (tech dependencies / items requires / ammunition) which overwrite the previous version?
But from what you just said, you can redefine a vanilla mission and it will be moved down the list?
*Still confused*
Either deleting or redefining the vanilla missions, if another mod (ex.: Mechtoid) adds a mission before yours then it will also screw things up and now you may end up with a mechtoid mission first month or something..