The Supreme Court in justifying their ruling that Section 3 enforcement by the states would be too chaotic and against the principles of federalism cited U.S. Term Limits v. Thorton, which was about states imposing stricter qualifications for Congress than the Constitution. I really don't get how it is even remotely comparable to Section 3 of the 14th amendment.
States used to appoint presidential electors without an election. And there are a whole host of different ballot access laws for presidential elections as third parties are well aware of. I would think Section 3 enforcement would be compatible with all of that. States have all sorts of differences on presidential election laws.
Trump probably shouldn't have engaged in an insurrection if he didn't want it applied to him.
The other case they cite Anderson v. Celebrezze concerned different filing deadlines for independent candidates versus the major parties. It was an equal protection clause case. Again not really comparable.