This actually makes some sense. Any time you mess with the framerate of the game, you'll have trouble adjusting. Whether you're conscious of it or not, your eyes identify the pitch based on the difference between frames as the pitch comes in. You mess with that difference, and you create a situation where you have to re-train yourself.
For example, I've been early a LOT since upgrading to the PS4 Pro, since my sub-conscious is still telling me: When the ball looks like *this*, that is when you swing.
Fastballs, off-speed, I'm early on most of it. Even 98 MPH which I used to find impossible to catch up to. My instincts haven't adjusted to the new environment. Even identifying pitch location has changed entirely for me.
I do think that framerate mode will, in the long run, be the best mode. You'll have consistency between stadiums in terms of framerate, leading to a more stable environment to teach yourself to identify and time pitches.
Lower frame rates will likely make pitches easier to identify, just like higher frame rates likely make pitches easier to catch up to.
All that being said, I'd probably still use HDR mode if I had the option.