The rule change codified what our crew has always done. I am the R, I have never switched out the ball.
Rule Book 1.3.2 Each team brings out the approved ball they want to use for a free kick or to start of a series.
Case Book 1.3.3 A/K is not entitled to switch in a "kicking ball" for scrimmage kicks. Our crew does not allow it.
Even before the new rule, allowing ANY official to reject a replacement ball, a replaced ball has to pass through, likely a couple of Officials hands, before getting into play (Wing Official, Umpire). If any of those hands didn't/doesn't like the way the new ball feels (pressure, surface, etc.) they should have ALWAYS been rejected and sent right back out. The old nonsense about special balls being snuck in to accommodate "special" pro QBs was likely nonsense, as multiple pro Officials get to handle (squeeze, touch) any ball on it's way from sideline to actual play. If the ball doesn't feel right, it shouldn't get in.
ANY ball, waiting on a sideline to get used, can lose pressure all by itself. The best protection against using a deficient ball, is STILL the game Official's hands passing it from the sideline to being placed RFP.