Looks like it has the wrong pickguard causing the p pickups to be shifted to the right. Try to get a warranty replacement. Note everything wrong. Sooner the better. Several months have passed since purchase. I used to have a D4, it was killer, couldn’t quite adjust to the neck-thru design.
Thanks. Took it to Guitar Center and the techs there gave me good vibes so I trust em. I might or might not be wrong about the whole red line of AP-5 being a lemon. He used a metal rod (taped at the end to prevent scratching) to locate the coils, and it seems that unlike the above schematic for an EMG P5 you can buy from the EMG website, these EMGs may be proprietary to the bass (makes sense, as you can't get a brushed black chrome P pickup from EMG). He found that the coils are offset, all shifted slightly to the B-side, unlike the customer P5 pickup.
They will bill ESP, but they think that hopefully just shifting it within the cavity to close that gap may be sufficient enough to properly place the coils under the B-string; he noticed it was about half off currently.
Whether he can move it enough without luthiering to make it look like this more idealized version of the ESP LTD AP-5 in candy red I found here https://reverb.com/item/81593624-esp-ltd-ap-5 is another thing...