Both Magic Bitboards and PEXT are run every single time Stockfish thinks of a Queen, Bishop, or Rook. Literally every, single, time.
Stockfish does something like 10-million positions per second or something. That's a lot of times the "where can the Queen move" analysis is run. Speeding that routine up by 50% or something (PEXT vs Magic Bitboards) really does make a difference in the great scheme of speed.
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Unless you're playing some fantasy-version of Chess (or maybe some extreme endgame where all pawns, queens, bishops, and rooks are dead... pawns because they might promote into a queen/bishop/rook), you'll be benefiting from selecting that PEXT version if you're on an Intel or Zen3 processor.