I had a similar thing happen with a Gretsch guitar that came with a P90 in the neck and a Broad’Tron humbucker in the bridge. The bridge humbucker was a bit muddy and did not have that classic Gretsch sound. So, I swapped the bridge for a Gretsch Blacktop Filtertron pup. When I soldered it together, I could tell the bridge was out of phase with the neck pickup.
Since, I am completely ignorant of the way electronics work in a guitar, I simply reversed the leads of the Filtertron bridge pickup. It worked and sounded good (in-phase). The only problem was that the neck pickup had way more output than the bridge.
I added a potentiometer and a Suhr-style treble bleed to neck pickup part of the circuit. Then, I broke one of the soldered wires shoving it down into the small cavity behind the 3 way switch. I got it right on 2nd try, dialed it in perfect.
I have no idea if the guitar is wired correctly, but it sounds great. There’s no buzz or noise, other than the typical 60 cycle hum via the single coil P90.
I figured Gretsch would keep their pickup wire colors consistent, but it did not work out in this case. Maybe, that Filtertron is counterfeit.