The Pixel smartphones' new partition system and boot images have been a hot mess for developers and tinkerers who like to push their devices beyond the specs written on the shipping box. But even though this has slowed down the release of custom recoveries and other mods, it hasn't completely stopped our beloved enterprising developers who probably thought of the whole situation as a nice challenge instead of an unsurmountable obstacle.
Just yesterday, Ethan Yonker (Dees Troy) released an early alpha of custom recovery TWRP for the Pixel devices, but that created a problem for those who were using the boot-to-root images made by Chainfire for the Pixels.
The devices would suddenly get encrypted after flashing SuperSU, which isn't something you want to happen spontaneously on your phone. Edit: actually, as Ethan corrected us, "the incompatibility comes from Chainfire using the recovery ramdisk to achieve system-less root on the Pixel devices. He would modify the kernel to always boot the ramdisk and used a modified init binary. TWRP also needed a modified init binary to achieve decrypt of FBE. The conflict occurs with the init binary." Chainfire explains that he and Ethan already anticipated the problem so he is able to release a fix quickly.
Long story short (and plenty of technical jargon that I would like to understand but don't have enough time to do so right now), SuperSU and TWRP now play nice together. There are lots of things to take into consideration and steps to follow closely to make sure you end up with a working device, so head over to Chainfire's post at the source link below. He also has all the download links you need.