A couple of things to note....
Technically speaking, rooting a phone is a modification that could void your warranty. If you send back a working Nexus 6 that as been rooted, they may or may not give you a hard time. But if the thing is completely junk... screen toast, won't power on, etc... they aren't going to send it to some phone CSI team to see if you rooted so you could run Titanium Backup... they'll mostly just recycle it without a second thought.
I supposed if you run into a software based problem that can be directly related to you breaking something yourself after rooting the phone... they might be a bit more strict since you wouldn't have been sending back that phone had you not popped the hood and started pulling at wires. But it is EXTREMELY easy to bring a Nexus 6 back to 100% bone stock.... soup to nuts... As long as the sucker can boot into the bootloader menu, you can plug that baby in and get it back to the exact same condition it was when you took it out of the box.
And you REALLY have to be an extremely accomplished fool to brick a Nexus phone... really... these things are pretty much bulletproof even to the point where there is a backup bootloader in case the primary gets corrupted (or accidentally flashed over with a kernel from another phone... hypothetically speaking... heh).
The Nexus 6 does not have any kind of flash counter/flag that gets triggered when you modify things. It DOES have a flag indicating that the phone has been rooted, but that flag will clear if you 'unroot' or flash a factory image or even a custom ROM that does not have root access baked in.
So if you needed to go back to stock... say you are trading in your phone, or it is functional but something broke (broken speaker, radio, etc). Going back to stock is as easy as getting the factory image from Google and following the instructions... or even easier grabbing a tool like Wugfresh's Nexus Root Toolkit and letting that do all the work.