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Which sadly begs the question of how a state can be denied its representation in Congress?

Easily answered. Article I, Section 5: "Each House shall be the Judge of the Elections, Returns and Qualifications of its own Members..." If Congress sets qualifications for seating members of states that participated in the rebellion then they are within their power to do so.

You answered easily, but your answer demonstrates an ignorance of basic constitutional law. Under Article I, each house is the judge of the election, returns, and qualifications of its members, but Congress cannot add its own qualifications and then judge them. Powell v. McCormack, 395 U.S. 486 at 550 (1969) Oh, and the Fourteenth Amendment was not "ratified" until 1868, so the prohibition in that against Confederates holding office in the Congress did not legally apply at the end of the Civil War when Lee surrendered at Appomattox Court House on April 9, 1865. If the Confederate States could not legally secede, then all of the Reconstruction laws were plainly illegal, including forcing them to pass constitutional amendments to regain their representation in Congress which constitutionally, could not be lost.

The unmistakable conclusion is that the South had seceded from the Union, and was only brought back at the point of a gun. Chase's opinion simply put a constitutional veneer on the war from the winning side, and, again, his opinion is counterfactual historically.