Clearly they think otherwise. It seems the believe they can reject it and they have.That was the case up to last year, with United and Bayern needing to find workaround solutions for Herrera and Martinez. Last year, La Liga changed the rules to make it straightforward and both Spanish and foreign clubs can just pay the clause.
Their excuse seems to be cause they don't believe that PSG can pay the clause and still be within FFP. Which is not their business (it is UEFA's).
If Neymar was going to go to Real Madrid for 1bn, and it would put Real Madrid in breach of their (La Liga's) rules, then presumably they would be able to reject it. That shouldn't be controversial. La Liga run the shop, after all.
So when PSG have rocked up to their office with a €200 mn check, which they would reject if it came from Real or Atletico Madrid, and they think they have the right to reject it.. then yeah, they've rejected it.
https://www.theguardian.com/football/2017/aug/03/psg-neymar-buy-out-rejected-la-liga-barcelonaLa Liga is understood to have also explained that it is unclear on the origins of the money and that under its regulations only Spanish clubs have the guaranteed right to buy out a contract. The league has repeatedly accepted buyout clause deposits from foreign clubs. It would not be able to reject the money if Neymar himself turned up to pay it.