I was also questioning how the new OneManArmy (release version) will work with polymorph.
However my guess is that they will chance the bonus you gain for polymorph.
I just don't see any other way how it should work.
As othwerwise if you would would invest 1 point into polymorph and then spend the 2 attribute points how should the system know which point it should take away ones you have a party of 3 or more.