The decision to publish the ledger is one made by the election administrator in the interest of transparency - there is no requirement to do so, but it is believed to increase public trust in the process. Unfortunately these types of transparency measures haven't necessarily been rigorously evaluated and the tradeoffs with ballot secrecy may not be favorable.
that is the real significance of this research to me, not really anything about the use of machines.
Some states do quite the opposite, e.g. seal ballots after the election and only allow inspection by court order. This has obvious benefits for secrecy, but then creates a lot of objections when people/organizations that doubt the election outcome are told that they cannot review the actual ballots (without meeting some threshold to justify such an order, which can be quite high since these rules were often put in place to try to counter pay-to-vote or voter intimidation schemes).
The existence of such a ledger isn't even required, but it makes it radically easier to audit the count process to detect errors. US election administrators demand a very high level of accuracy in vote counts (higher than what is typical in a lot of other countries), so in hand-count processes it's common to tabulate each ballot multiple times, and with machine tabulation there is usually some kind of automatic recount or risk limiting audit, either by retabulating with separate machines or hand-counting a sample. All of these are much easier processes when you can correlate a ballot to the previous time it was counted, so that errors discovered in auditing can be tracked to the specific ballot that was miscounted and corrected. Otherwise, if you count a batch of ballots twice and get different results (which is virtually guaranteed with hand counting), you will have to recount the entire batch over and over until you get satisfactory convergence. There are several different methods of doing this: some jurisdictions serialize ballots when they are printed so that tabulation can be tracked by that serial number. Other jurisdictions avoid this potential secrecy hazard by only serializing ballots after initial tabulation (e.g. ballots pulled for a sample audit have sequence numbers added on stickers or hand-written). Some tabulating machines can add sequence numbers as they run. All of these have different considerations as far as reliability and secrecy, but unfortunately there is next to zero funding or political interest in researching these issues and applying the resulting knowledge. The result is that everything is highly variable from state to state and some states continue to use processes that are known to have significant defects, most famously Louisiana with its ongoing use of non-auditable DRE machines (the only state that continues to do so).