(I'm not defending the method you describe from Texas where there's no physical proof to audit against)

I was listening to something specifically talking about California counting mail-in ballots. They said California took longer than most states because it's big, it has liberal laws about eligibility (counting provisional ballots) and citizens are pretty sloppy about filling in mail-in ballots. They described coffee and spaghetti stains obscuring the choice. They will fill out "clean" ballots in pairs with their best guess. I'm sure that's a small number of ballots.

When I've voted in person they deliberately have me feed my ballot into a machine to confirm it was valid.