But all of those already exist in GT6. So why add them, when they are already there?
As for Shredder Recipes in NEI, yes they are mostly autogenerated once you actually put the item into the Shredder, Stuff like that saves about 20 minutes of Minecraft startup time.
And you found the Buckwheat to Flour Recipe there, and that Flower can be turned into Flour IRL too.
Hrrm, did you make the Duration of the Recipe you added different from the Duration of the Recipe you removed? Maybe the one MineTweaker added uses the same Config due to that coincidence.