Ok, the calculator assumes this is the case, so your input is correct. If you were to play with black bars the correct way would be to enter your monitors native resolution.
The conversion method is what's throwing you off then. Since you play stretched it means that only the horizontal FOV is stretched, and since you are matching using the vertical FOV you get the same sensitivity (since it's identical for the two games). This will be correct for the vertical movement, but you probably move more horizontally which is why it feels off.
I'm guessing Apex fels too slow? Try one of the horizontal methods, they should better fit your setup.