Last night, the first alpha release of TWRP was announced for the Google Pixel and Pixel XL. We delved into much detail about the release, including the changes to the installation procedure as well as what’s new and what’s broken. One of the caveats we mentioned in the article is that installing TWRP would cause SuperSU to no longer function.
Installing TWRP at this time will remove root if you are currently rooted. A SuperSU update will be required to allow TWRP and SuperSU to co-exist.
As we explained in an addendum to the article, the reason that installing TWRP would remove root is because the method used by Dees_Troy to allow TWRP to decrypt the data partition involves modifying the same init binary which is modified by Chainfire to achieve systemless root. Thus, by installing TWRP the changes made to the init binary by SuperSU would be overwritten. In order to not cause any conflicts, Chainfire himself recommended that if you currently run SuperSU and plan on installing TWRP, you need to first flash the stock boot image from the Factory Image. The two developers have been in contact regarding how to resolve this conflict, and today Chainfire has released SuperSU v.278 SR4 which fixes this issue for the two Google Pixel phones.
In the update, Chainfire mentions that this update will allow for SuperSU to be flashed on top of TWRP (and not the other way around). His boot to root script will now no longer conflict with the init binary changes made by TWRP, but until TWRP is updated the reverse isn’t true. So for now, you will need to first install TWRP and then flash SuperSU once you’re in the recovery environment. This is assuming you want to have both SuperSU and TWRP, of course. And to reiterate, if you are already rooted with SuperSU installed and want to now have TWRP as well, you will need to first re-flash the stock boot image, then install TWRP, and finally re-install SuperSU within TWRP.