Dred Scott was a resident of Missouri when he sued for his freedom. The Scott vs. Sanford case was decided in 1857. So this case has nothing to do with the Confederacy. Missouri remained a Union slave state throughout the war.
Can you cite instances where the CSA “used the federal government to enforce their own determinations on states that differed from them”?
Yes. Dred Scott Fugitive slave laws.
They used the force of federal government to make other states accept their view on humans as property.
Dred Scott applied to all states.