If a state's government chooses to organize its election in such a sloppy way that unverifiable ballots are co-mingled with verifiable ones (poisoned well concept),
Since that didn't occur in any state, it's a moot point.
should the US Supreme Court intervene?
There's no basis for the U.S. Supreme Court to intervene.
Or should each state be allowed to decide for itself how much error risk it is willing to accept with its own vote count process?
The U.S. Constitution gives to the individual states the duty of deciding their own election processes including the contesting of elections. The role of the federal government is extremely limited. What kind of additional federal control of your state's elections would you want?
My guess is the SCOTUS will likely side with states' rights on this matter
Given the lack of any basis for the U.S. Supreme Court to intervene, that's a safe bet.
even if a state violated its own laws.
None did so, but each state has a legal process to determine and contest both elections and election processes. Only if federal laws or federal constitutional issues are asserted, would a federal court consider whether or not to hear a case. Given the difficulties of overcoming the issues of standing and justiciability under the political question doctrine, there is little likelihood of a case surviving beyond an initial hearing before being dismissed.