We conclude that States may disqualify persons holding or attempting to hold state office. But States have no power under the Constitution to enforce Section 3 with respect to federal offices, especially the Presidency.
To be fair, the government has always set criteria for being on the ballot. For example, to be US president you have to be at least 35, a natural citizen, and have live in the states for at least 14 years.
Not being an insurrectionist is also part of that criteria. We’ve just never had a presidential candidate that has needed us to consider that part of the constitution.