It's a little weird, now that I looked into this more deeply, because while that's what the referendum question said on the ballot, the law that put it there is https://senado.pr.gov/Legislations/ps1467-20.pdf and defines the "yes" and "no" answers to have the following meanings, respectively (page 31, lines 6-15, translation from Spanish mine):

- Yes: I demand that the Federal Government immediately recognize the equality of my rights and responsibilities as an American citizen with statehood in permanent union with all the states of the Union.

- No: I reject permanent union with statehood and demand that the Federal Government immediately recognize the sovereignty of Puerto Rico separate from the United States of America with a "Treaty of Independence in Free Association" or with "Total Independence".

Notably, that excludes the status quo as an option. The part right after that says:

  In case the statehood "No" ends up as the majority choice, you must
  immediately start a process of transition to recognize the sovereignty
  of Puerto Rico separate from the United States of America with a
  "Treaty of Independence in Free Association" or with "Total
  Independence", following the description in this law.

What I don't know is to what extent people actually attached those meanings to the choices and hence whether it affected the vote at all, but defining the "Yes" and "No" answers to that question to have those specific meanings is a bit underhanded and quite unfortunate.