The article you linked to provides a pretty good explanation, directly from Reed Galen, a strategist for the group:
He said that for the most part, Republican dissent has been weak and that GOP lawmakers have been silent as Trump ran up the debt, ordered the police to move on peaceful protesters outside the White House and declined to challenge Russian President Vladimir Putin for offering bounties on U.S. forces.
“They should have seen themselves as members of the U.S. Senate and put the country first,” Galen said. “If the head of the party is Donald Trump and you disagree on policy, politics and decorum, and the best you can summon is that you’re worried and concerned and hope that he does better, that’s not opposition."
Senator Collins claims to have opposed Trump, but her opposition has been all talk and no action. She certainly has claimed to be "disappointed" with Trump many times, but when she's had the chance to take any action, she has refused.
The most glaring example was probably Trump's first impeachment, where she offered a laughable excuse for voting to acquit:
Collins said "I believe that the President has learned from this case" and that Trump "will be much more cautious in the future."
You mention similar statements, her criticism of the Lafayette Park incident and her claims that he's unworthy of being president, but were these statements backed by any action? Again and again, she delivered mild disapproval, while supporting his court nominees and voting with the party line to block any efforts at accountability.
The intensity of the opposition to Trump doesn't come from policy differences, but from the understanding that his cult of personality and strongman governing style threaten the survival of American Democracy itself, a view that has been vindicated by his actions since losing the 2020 election. You can't oppose a threat to democracy with mild disapproval, and since that's all that Senator Collins had provided at the time of the election, she's just as much an enabler as any other Republican. And, as an enabler in a relative Blue State (Maine went for Biden by 9% in 2020), attacking her was, at least in theory, the best chance at actually beating a Trump enabler.
You mention that "the Lincoln Project would prefer a Senate full of Susan Collins'." That may be true, but if every Republican was like Susan Collins, there would be no Trump. Collins should be judged by how she acted in the real world.