The court's confusion might be forgiven. On one hand, they correctly rejected that case in Texas vs Pennsylvania stating Texas has not demonstrated a judicially cognizable interest in the manner in which another State conducts its elections.. Yet here, they have clearly indicated they will rule against Colorado for fear affirming Colorado's decision would interfere with voter rights in other states. When you are opportunistically picking and choosing your principals, it's hard to maintain the appearance of consistency.

I don't think it's that tough. States are expressly given the right to have disparate means, methods, and manner of conducting their elections. But qualifications for federal office are set by the Constitution, and are required to be uniform throughout the country.

So states are perfectly free to choose whether to have drop boxes or not (for example), and no other states have an interest in their choices on that matter. But states are not given any "discretion" in setting requirements for who is allowed to run for a federal office (U.S. Term Limits v. Thornton). The rules for elections can vary (wildly!) from state to state, but the criteria for candidate qualification are uniform and limited solely to those set out in the Constitution.

From oral argument, it looks like the Court is likely to focus on whether state legislatures and state courts are permitted to have any role in determining candidate qualification under the Constitution. IOW, if you think that a candidate is wrongfully running for a federal office in violation of a Constitutional requirement (say, they're 32 years old or are George W. Bush), the only appropriate mechanisms for enforcing that are federal. Either you're supposed to go to federal court to enforce the federal restriction (if it's self-executing), or you're supposed to have a federal statute which is enforced in federal court (if it's not). State courts don't have the authority to decide those matters.

The Constitution expressly embraces that States might differ on the best way to conduct an election, but not that they could use their own differing standards for what constitutes "aid or comfort to the enemies" of the U.S.