The pick up sounds interesting and I've read some folk have flipped the coils as I believe they have A5 and A3 to even out the sound.
FYI there's been a lot of confusion regarding the pickup design.
It was widely reported, during the original launch / promotion / reviews / reactions that the E&A half of the pickup was AlNiCo II, and the D&G half was AlNiCo V.
Some people were so sceptical of that idea on paper, and some seemed so offended by the idea of not having AlNiCo V on the E&A side, that they swapped the halves around - and indeed some people said they preferred the overall tone that way around.
I took mental note, in the event that I ever decide to change the pickup, to swap the halves around first, and give it a try (for the most part I'm perfectly happy with the stock pickup).
Anyway, I happened to notice several glaring errors in the Fender user manual, as well as a description of the pickup that completely contradicted the popular wisdom about the V-Mod II P.
So I contacted Fender, and after an investigation with engineering department, confirmed that in actual fact :
E&A = AlNiCo IV (yes, 4!)
D&G = AlNiCo II
This was a surprise, but actually makes a lot of sense given my experience with the sound.
Whereas AlNiCo V imparts a particular (desirable) character; AlNiCo IV is pretty transparent, without adding any character - which tallies with my feeling that the instrument essentially sounds the same both acoustically, or plugged in.
The AlNiCo II half would, as you say, balance out the tone, with a softened treble response.
Whilst there's no doubt we all like, and are accustomed to, the sound of AlNiCo V pickups, the thing I've noticed with the Am Pro II is that if you pick one up, and it sounds great unplugged, it will sound identical plugged in; if you pick one up and it doesn't sound so great unplugged, it's not going to magically sound any better plugged in - there are no surprises, and you have a good benchmark for the results you'll get if you decide to swap for a more traditional "character" pickup.
Even if I didn't like the covers - for that price I'd be willing to accept the resultant "vandalism" to the bodywork .
Great score!