When South Carolina says in 1860 they want to quit the union, they are saying the US court system doesn't have jurisdiction

Naw. The State of South Carolina is in the Union (and under jurisdiction of the Federal court) until that court gives them permission to leave the Union. At that point it no longer matters who does or doesn't have jurisdiction over them.

may hereafter...be formed out of the territory thereof, which shall be entitled to admission

But not required. They could split off the whole state except one little corner next to Louisiana (East Texas ain' hardly *real Texas anyway) and then not bother to join the Union.