Section 4 of Article One grants the states the power to regulate the congressional election process but establishes that Congress can alter those regulations or make its own regulations.

That's it. The Constitution of the United States hands off elections to the states.

You said...
What I don't understand is why in the world the constitution was not followed and the ballots kept in the care of those originally defined as the ones to maintain the security of the ballots.

No such clause exists.

The Arizona audit was not an official recount and cannot change the results of the election. The Arizona Senate voted to hire outside contractors to search for possible fraud in the elections. The US Congress has no say in the matter unless other Constitutional Rights are/were violated.

NOW...there's going to come a point where all these new restrictions on voting begin to infringe on the Constitutional Rights of citizens to vote. That's where the US Congress could step into the fray.

Arizona and its hired auditors can do as they please and as their laws prescribe with their ballots. The voting machines will be junked and replaced at taxpayer expense.

Section 4 does pave the way however for congress to give the mechanics of voting and tallying to the Post Office. States would continue to manage the rest of the election process.

Good coffee, good weed, and time on my hands...