The deal had an "economically feasibility" provision that provided for a second negotiation if games were not going to be played without fans. This was explained to the MLBPA before the March 26 deal was finalized:
https://nypost.com/2020/05/19/mlb-thinks-email-is-smoking-gun-in-salary-fight-with-players/
BTW, as part of the March 26 deal, the owners agreed to pay a $170 million advance to the players in 2020 salaries which they would keep if there was no season, and the owners agreed that 2020 service time would count if there was no season, which was huge for young players approaching free agency and arbitration eligibility. So, the MLBPA already received key concessions in the March deal. Why would MLB agree to pay pro-rata salaries to the players if some or all of the games were played under conditions when at least 40% of the revenues in ticket and concession revenue are lost for the games that are played without fans? That would make no sense, and was expressly explained before the deal was signed and $170 million was paid.