The article you links to reports that Statehood won the 2012 referendum (majority voted no to current status, and Statehood got a majority of votes for the alternative status), which Congress chose to ignore, and overwhelmingly won the single-stage 2017 referendum.
So, no, the issue is not “they have had opportunities to begin the process to fully opt in and haven't done so”.
None of the referenda have been binding referenda (which Congress could provide for, but has not) and most of them except the 2012 two-stage one have been structured, (often at the direction or request of the US federal government) to avoid a clear win for any option other than status quo (including the 2017 one, which had an additional option added at the request of the Trump administration to split voters opposed to the current status.)
Of course, the 2017 referendum was only held at all because the Statehood won by the terms of the 2012 referendum, and the federal government ignored it and the requests by the elected bodies of the government of Puerto Rico to abide by it.
The idea that Puerto Rico is not a state because the people of Puerto Rico have not availed themselves of the opportunity to choose to become one is false.
Opinion polling put Statehood at 52%, with a 3.2% margin of error. Sounds close, but the referendum had 3 choices, and neither were very close.
It seems like those opposed to Statehood realized they'd lose as they split the vote, and ran a boycott campaign, effectively turning it into a yes/no vote on statehood, with the fringe benefit of claiming all non-voters as on their side, which going by 2012, is a free 20 percent of the vote.
For better or worse, there's not really an objective way to evaluate this state of affairs =/
We could do what we do with every other election, and treat nonvotes as irrelevant to the validity of the outcome unless they result from people being improperly prevented from voting rather than voluntarily abstaining, whether in protest or otherwise.
Obviously "what we do" is influenced by Congressional makeup and how PR alters it, but that's pretty much what the diff between a binding and non-binding referendum means in practice.
And maybe forcing the issue is a bit too colonial, optically.
According to your link, in the 2012 referendum, the majority (61.11%) of votes were for statehood, but congress decided to ignore the referendum because of the large number of blank ballots (500k).
Both referendums were widely boycotted for various reasons by no voters. The only people who voted were the small minority who wanted to become a state.
The 2012 election had 78% turnout with valid ballots in the question of whether or not to continue the current status, on which a majority voted to reject the current status, and 56% turnout on the question of alternative status, on which a majority chose Statehood.
On either question, the turnout was better than several US Presidential elections (and on the first better than any recent Presidential election.)
There were significant boycotts of the 2017 referendum because of the wording of the title, but in any other US election, we don't ignore election results because people choose to abstain.
It looks like approximately 1.8 million people voted on the first question, and 1.36 million people voted on the second. And in 2016 Puerto Rico was estimated as having a population of 3.4 million. In light of that, 1.8 million votes on the first and 1.36 million votes on the second seems fairly similar to the normal voter turnout in the U.S.
So no, it doesn't sound to me like a "small minority" of people were voting.
EDIT: This is talking about the 2012 referendum.
EDIT 2: It occurs to me that 3.4 million isn't the voting population, it's the total population. So the voter turnout is even better than it looks initially.
A small minority of Americans voted for Trump. Should we have ignored the results of the election because only a small minority of sour grapes shouldn't make that important a decision for the rest of us?
So, no, the issue is not “they have had opportunities to begin the process to fully opt in and haven't done so”.