After a lot of trials and errors, I managed to run Pokemon Go v0.39.1 on FP2 OpenOS 16.08 
The trick was to remove the su binaries in /system/bin and /system/xbin, then install the correct versions of Magisk, systemless Xposed and phh superuser…
I put the details in this post : How to be able to install and use any app on FP Open OS [meta discussion]
Now I’m able to play again !