Oh. Did he choose to partner with Nintendo? Or Phil Spencer did?
It makes sense since Microsoft is not doing anything with the IP, so they wouldn't really have any use for them in the game, unless Nintendo asked specifically for Banjo & Kazooie - which I very much believe was what happened.
It fills my heart with joy thinking that Nintendo saw the amount of love still around for B&K (probably because of the ballot) and decided to go get them.