Nearly every game I know of that ties things to the frame rate are games that require frame perfect inputs for many mechanics so I assume it’s just a lot easier to ensure the timings are predictable and achieveable by a wide range of hardware than it would be to base everything on the internal clock or some other time measurement that can vary depending on the machine.
My only experience with programming time based things is in doing mission creation and scripting for ARMA, but it has very much the same kind of issue where if you want everyone playing on the same server to have the same timings for events and such, you can’t just use the game timer. It would be several milliseconds off every client to the server making it unpredictable and desynchronized from all other players.