I had this phase issue on a Telecaster that we installed a Seymour Duncan Quarter Pound into. First we had the neck disconnected so there was no issue. Then my friend decided to replace the defective wiring and have the Fender neck pickup connected again. I looked up the colour codes but is seems that Fenders can be reversed with the colours in some cases and I had it wired backwards. We reversed the wiring on the neck pickup and it was fine.
There may be some confusion because on the Seymour Duncan pickups the black is hot whereas on Bare Knuckles black is ground
On Seymour Duncans the green is ground.
On Bare Knuckles the red is hot.
In both cases the bare wire must be grounded as well.
On Seymour Duncans the other two wires are white (north finish) and red (south finish), whereas on Bare Knuckles they are green (north finish) and white (south finish). These are the wires you use for various switching options.
I think you can see the scope for your tech getting confused.
Check that the hot wire for the SD is black and the hot wire for the BKP is red on your guitar. If you are not using coil taps etc those wires should be soldered together and insulated with shrink tubing, and the other wires should be grounded on a pot.
To keep the option of the phase reversal sound you could install a push-pull pot on your bridge pickup using the following diagram from BKP:
https://www.bareknucklepickups.co.uk/upload/support/1_hum_4_con_pushpull_pot_phase_reversal_with_another_hum_c8e3961.pdfThis mod simply inverts hot and ground and does not involve the green and white coil split wires.