Physical security (or, if you prefer, "chain of custody") is essential to all elections. Even if we're talking about hand-marked and hand-counted paper ballots, we still need to ensure that ballot boxes were sealed properly, transported properly, and guarded properly. Of course, when you add computers to the mix, physical security is even more important. This is an important reason for having post-election audits, like the RLAs we talk about in the linked article at the top of this post. An efficient post-election audit allows for discrepancies to be discovered before an election result is certified.

Physical security remains crucially important for risk-limiting audits as it requires the set of ballots cast by voters not to be altered (reflecting the set of legitimate cast ballots).