Until 0.15 when the new API for mod configuration is available, the easiest way (for end users) to assemble a mod pack is to use a config mod which sets up other mods in the desired way.
Could SCT be changed to have the loading of specific recipes into data-updates.lua? This would allow another mod to set the variables in their own data.lua before SCT loads the recipe overrides, allowing easy external config for this mod.