Until OP started this thread, I had never heard of Greg Palast. It looks like he has received acclaim for investigative journalism on some prior matters, including election fraud in Florida.
As to whether the subject matter of the linked report is accurate, it is difficult to say. Almost all of the readily available information on the internet links back to Palast's report (as opposed to independently verifiable data), or duplicate postings on other websites -- with or without accreditation to Palast. In particular, many sites quote identical language from a report by Baxter Dmitry. http://yournewswire.com/california-primary-results-in-voter-suppression-election-fraud/ One of these two, Palast or Dmitry, is plagiarizing the other. I'll give Palast the benefit of the doubt that he is the original.
For being a flashy "look at me, I'm Sam Spade" investigative journalist, Palast does shoddy work in this expose. There is little accreditation for his sources. For example, Palast says "Poll worker Jeff Lewis filed a description of the training in an official declaration to a federal court" -- what case? what court? I was able to find only one federal lawsuit related to 2016 California election fraud: Voting Rights Defense Project, et al. v. Depuis, et al., filed in USDC for the Northern District of California on 5/20/16 (almost three weeks before the California primary). The case sought an extension of voter registration, and was rejected by Hon. William Alsup a week before the primary. There does not appear to be any declaration from a Jeff Lewis in that case.
Regardless, the quoted text of Lewis' declaration does not necessarily match Palast's interpretation or the general theme of Palast's report. If someone asks where the presidential candidates are on an NPP ballot, the purported instructed response is that NPP ballots do not have presidential candidates on them. This is true. That is not the same thing as saying "NPP voters can't get Democratic ballots" when an NPP voter asks "how do I get to vote in the Democratic party primary?"
Palast accurately quotes the California Election Officer Training Manual at page 49: "A No Party Preference voter will need to request a crossover ballot from the Roster Index Officer. (Do not offer them a crossover ballot if they do not ask)." That is not the same as Palast's interpretation: "They are ordered not to breathe a word that the voter can get a “crossover” ballot that includes the presidential race."
Compare the California Secretary of State's website (http://www.sos.ca.gov/elections/political-parties/no-party-preference/). It states: "How to request a party ballot? The NPP voter may ask their county elections office or poll worker, at their polling place, for a ballot for one of the above three parties. An NPP voter may not request more than one party's ballot."
To me, it seems pretty straightforward. If you're registered NPP, you are allowed to vote in the Democratic primary (but not the Republican, because the GOP does not authorize that). The default is that you are given an NPP ballot. The NPP ballot does not have presidential candidates on it. If a voter asks where the presidential candidates are, the election worker's response is that an NPP ballot does not contain presidential candidates. If a voter asks for a Democratic ballot, he or she is given (a "crossover") one. If a voter does not ask for a Democratic ballot, election workers are not supposed to give one or suggest there is an alternate option.
That does not sound fraudulent or nefarious to me. If Palast is onto something, he should do a better job articulating it and citing support.