The conflict is that the States in question did not follow laws passed by their State Legislatures as required by the US Constitution.
A State Governor, or State Court, cannot dictate election policy, and only the State Legislatures can, and through legislation.
Let's set aside the fact that the Texas governor changed election policy through order and not by legislation. Most (maybe all I haven't examined the entire thing with a fine tooth comb) of the "problems" that it alleges had already worked it's way through the courts of each state which determine the interpretation and constitutionality of the state laws. Some of it is just meaningless nit picks. For example, they take issue with Georgia calling voters who have issues with their ballots that need to be cured. The law states that they need to be notified in writing. Okay, so the state did both, what's the problem?
Secondary ... The dictates were not followed/enforced equally by all precincts within each State in question.
That violates the Equal Protection Under the Law in regards to the vote and Articles in the Election Rights Act.
I don't know about that. I know for sure they take issue with Pennsylvania not applying the law equally. They state that voters in different counties were not given the opportunity to cure their ballots because some local officials decided not to inform people who had issues. Pennsylvania law is silent about the ability for people to cure their ballots, and the state officials did notify local officials that it is a good idea to do. These were not different sets of laws but just dereliction of some local officials to help their voters. If the law does not mandate or forbid something, it cannot be unequal application of law.
There's a lot more to this lawsuit including some very shoddy claims of fraud from some very poor quality analysis.
But the points you raised above are central to this rebuttal. These policies were changed before the election and voters went to the polls operating under these circumstances. Deciding after the election to challenge these issues would remove the votes from many millions of voters. For what? For what harm are they claiming?