I tried the coils both ways in the P5, which came stock, before ordering the P6X (EMG make all that swapping really easy). I think both ways work about equally well, so I went back to the stock wiring when I decided to put the instrument up for sale. Of course that's when I finally got the setup just right

I don't care for the sound of either pickup on its own but they sound pretty good together, so I won't mind keeping it at this point
Here's how everything lines up (pickup angles are likely different now, but you get the idea):
View attachment 4385269
This picture convinced me to try flipping the pickup halves (so that the half closer to the neck would pick up the middle string), but I don't think it made much difference.