Get root permissions is now well-founded on Android; do it in a “transparent mode” is another thing, especially since Android 6.0 Marshmallow started to become a bit allergic to changes. But it seems Chainfire did it again, he got root permissions without changing the / system folder.
Boot images for all Nexus with marshmallows and a special package for SuperSU TWRP are in fact already available on XDA.
One advantage of this method is the possibility in receiving OTA updates: simply flash the original boot partition, which is a very fast operation, that does not compromise user data, and the fact that fewer changes are made to /system, guarantees to have a system not compromised.
But note that not all SuperSU options are present in this way, and that has not yet been verified to work correctly on devices encrypted. Anyway on XDA you find all the files needed to proceed and we do not doubt that will come soon packages for other smartphones. Whether or not this will be the future of the methods of root, we’ll find out only after some time.
Stay tuned on Twitter @roccocannale for further updates