Amazingly, I happen to own the very rare same exact 1970 JS II that NMiller owns, as well as the same exact 1968/69 SF II bass w Bisonics that he recently sold (as well as the same exact 1957/58 66J amp- all 3 identical to yours- amazing!)
yes the JS II and SF II basses I own are wired out of phase.
the reason 2 Bisonics are wired for reverse polarity and 2 humbuckers are not is quite simple...Bisonics are single coils. In certain situations they can and will "hum" or "buzz" on their own in neck or bridge, or together in middle, but with reverse polarity, in the middle position with both pickups engaged all or the majority of the humming/buzzing should be gone. It is a safety net for performing. The tone of the individual pickups should not change (although I am not here to debate that) and I'm not sure how much the "reversed polarity middle position tone" changes...but the hum should be gone in the middle position if done right.
The reason humbuckers are not wired for reverse polarity, is because the inherent nature and purpose of a 2-coil Humbucker is to "buck the hum," hence the reason humbuckers don't hum at all (or shouldn't) on their own or in any configuration. Therefore, reverse polarity is not necessary, and middle position output is not lost.
In the case of NMillers JSII (of which I own the identical bass), one pickup is single coil (neck), and one is Humbucker (bridge). So no hum in the bridge whatsoever. Now with reverse polarity, the middle position gives a second "no hum option." Also, this particular configuration was quite rare and transitional, they may have simply been following the "double Bisonic formula" for this small batch of Bisonic/Humbucker basses.
not to say the Bisonic on its own has any issues or hums at all- this will vary room to room and depends on outlets/wiring/grounding/dimmers/switches etc...
so in conclusion, yes Happy Face your M-85 II with 2 bisonics should be reverse polarity, as you recently found out it is. I don't understand why you would want to "un-reverse" the polarity. I suggest to leave it the way it is, unless I've missed something here, or elsewhere.
reverse polarity is very popular with telecaster guitars for the reasons described above. Many teles, or most teles, are wired that way by Fender at the factory from day one, at least in recent years.